It can be the most monotonous part of the game, doing a level over and over to get the right animals for your Chao. Here are the best locations to get them fast. With four or five animals to be had at the least, you need only play the level twice to get a full set of ten.
Note: I prefer not to use Tails and Eggman to collect animals. The animals chase you if you free them, and with Tails and Eggman their mecha are so clunky that they will often pick up the wrong animal while trying to get away from it. Also, when they're in cramped quarters it can be very difficult not to pick up Chaos Drives. If you're going for ten of the same kind, this is annoying. Where Tails and Eggman shine, however, is collecting Chaos Drives. Mission Street and Lost Colony are the best levels for doing this.
Pick the animal type you want
Swim|Fly|Run|Power|Luck|Legendary|Ghost
Yellow type: Rouge, Dry Lagoon
Penguins and sea otters are available here. If you want seals instead, try Knuckles and Aquatic Mine for seals and penguins.
Free the turtle, then continue straight ahead and move into the corner. The first Chao box is here. Get the key and then turn left and climb the wall beside the big statue. There's a GUN bug at the top; kill it and break the second Chao box. You'll probably have to dodge a peacock and a sheep, but there should be at least two Yellow animals here.
Continue on around the ledge. At the other side of the room is a tank; kill it. There's a pipe here beside the metal boxes, so whistle for a sea otter.
Ride the turtle down to the other part of the level. When you come up, turn left and go to the shallow pool at the end for another sea otter.
Turn right around and go to the other end of the area. There's a deep pool here; dive in for another penguin or sea otter.
Now go back to the middle part of the level, and dive into the water. A turtle is swimming around below; get behind its tail and press B to hold on. It will take you through a channel with a strong current; press A to let go at the other end and float up. You'll find a penguin on a ledge here.
Purple type: Knuckles, Wild Canyon
Peacocks and condors are available here. If you want parrots, try Rouge and Security Hall; she gets parrots and condors.
Start by grabbing the Chao box on one of the pillars in front of you, then fly up in the wind current to the top part of the level. Like Dry Lagoon, there are two parts to the level here. Take the one with the horizontal stone spars jutting out above; you'll find a condor at the end of one of the spars.
Go on to the end of this area to find a large statue. The second Chao box is at its feet: break it and just glide to get the peacock and condor safely.
Turn right around and go to the other half of the area. A peacock is flying around near the stone head here.
Now go back to the central area and fall down onto the sand. Explore the edges: in a nook you'll find a pipe which will give you either a condor or a cheetah.
Green type: Shadow, Radical Highway
You'll find boars and cheetahs here, and you'll find a lot of them, making this the best place to get green animals. If you want rabbits it tends to be easiest to do City Escape over and over.
You start with a series of grinds, roads and speed ramps. When that's over you'll find yourself on a platform with a GUN drone and a bunch of wooden boxes. Kill the drone and break the boxes for a cheetah or boar.
Turn to the left now and go around the side of the area; you'll find the first Chao box here. Take the key and continue round to the back of the ledge. A boar is walking around beneath a bulldozer.
Climb up and continue along a stretch of road until you see a bug and a GUN robot. Kill the robot, but don't go on to the upper area yet - on the rail behind the robot, a cheetah is walking about.
Go up, take the rocket and run along another series of roads and speed ramps. Springs will fire you round and round a great cylinder; when you come out the other side, you'll run along another road and reach an area with a number of bugs floating above a series of ledges. Don't attack the bugs; fall down and walk along. The second Chao box is on the first ledge here, and it should contain two green animals.
Continue on down a ramp and up the spring. At the top, turn sharp left and get over the rail; you'll see a cheetah under the heavy machinery.
Continue on and take the rocket. As you fall, angle yourself so you land on the top of the tollbooth. A boar is walking around here. NB: if you get it wrong or fall off, you can still get up onto the tollbooth by jumping on the rail at the edge of the road, and jumping up from there, but it's a bit tricky.
Continue on along anothe road and speed ramp deal, but don't take the trick ramp; go straight down to the very bottom. There's a cheetah here on the left.
Break the boxes to reveal a spring; take it to get back up on the higher level. Kill a GUN robot and move on to the spin poles and pistons. NB: if you don't want Chaos Drives from the bugs here, you can jump on the bridge support and run up it. Take it slow if you do. At the top, there's a pipe; whistle for a boar.
Now grind down the left hand rail. You'll land on some brown boxes; jump up onto the higher ledge and turn back. There's a boar here behind some construction rails.
Go on almost to the end of the level. When you see the Goal Ring, look around the tollbooth, and you'll find one final boar on the right hand side.
Red type: Shadow, Sky Rail
The level is tough, but Shadow gets both bears and tigers. If you want something easier try Eggman and Iron Gate for tigers and gorillas.
You grind down the first rail and land on a platform. Don't take the spring; turn back here and look behind the pillars for a bear.
Continue on to the end of the section of ledges; ignore the pipe, it's always a condor or a sheep. Jump onto the platform with the rocket, but don't take it - jump across again to get the Chao box. Then jump back and take the rocket. You'll land on another small platform with a speed boost; step on it to be sent whizzing along another rail. At the end you're on a small platform with a grind rail that leads down to another ledge. Stop on the first ledge; you'll see a pipe. Whistle for a tiger.
Jump off and homing attack the spring to be sent up to a new area with a bouple of flying GUN robot. Kill them or not, it doesn't matter, but take the two heli-springs up to another platform with a continue point. There's a tiger here.
Go on the next grind rail, and get ready, because at the end of it you have to jump as far forward as you can and homing attack the spring bug. With luck you can land on a tiny ledge with a couple of grind rails and a tiger.
Jump off and fall down to the area you'd otherwise have landed in. Go left and ascend a series of ledges with heli-springs. A bear is in a pipe here.
At the top, a speed ramp leads on to a continue point and another set of grind rails. At the end you'll land on another platform. Dodge the flame throwers and assorted nastiness here and take a heli-spring up. There's a tiger here hiding behind a dead tree.
Blue type: Sonic, City Escape
This is the only one to consider for the blue animal type: you can find all three blue animals here!
After going down the first series of slopes, stop in the green area and turn to your left. You can jump up on the wall here. Behind the hedge you'll find the first blue animal, a raccoon.
In that same area, break the four brown boxes by the stairs and you'll see a pipe. Stand next to it and whistle. The animal is either another raccoon or a rabbit, so be prepared to evade if it's the latter.
Continue on to the end of the area and down a section of stairs with grinding rails. Next is another series of slopes leading to some springs and ledges. Stop at the bottom. There is a rabbit on the right hand side; don't pick it up, but break the black car on the left hand side to find a skunk.
Next is another series of slopes with a super sneakers to be had. Go slow down here and stop at the arch, where you'll find another raccoon wandering about.
Down some steps you'll reach a place with two robots and an upward ramp. Go up the ramp. The box with the Chao Key is here - take it, and then double back, keeping to the wall, so that you fall into the fenced area. There's a trash can here; whistle to get your first sheep.
Take the spring and continue on down the grassy slope. A very cool segment follows with Sonic running down the side of a skyscraper. At the bottom you'll hit a spring and then two spin poles. Fire yourself off both poles (if you fail you can walk back and hit the springs again), and you'll reach a top platform with another Chao box. Break that for two or three more blue animals (just dodge the rabbits). There's another sheep in the trashcan on the ground below.
Cross the pit with the pistons and bug, and you reach another area with stairs and grinding rails. Go down it and cross the next area, but before going through the gate to race the truck, take a look behind the hedge. Another sheep!
Gold type:
There are only two gold animals per level. One is in the third Chao box, and the other is hidden.
Dragon: use Knuckles in Aquatic Mine. The first Chao box is in the room above you when you start, accessible by jumping on the lifting cable with the water level at 1. Look behind a piece of wood for the Chao box. Set the water level to 3 with the switch in this room, then fall down the hole and go right to the bottom of the level. Run around in the water here until you see an opening; go in and get past the spiky GUN robot to see the second Chao box. Climb up again to the top and fly around until you see a fenced off shaft with "CAUTION" and two images of ghosts. Go down the shaft. In this room, climb the wall to your right and move along; the final Chao box is on the rafters here.
To get the hidden dragon, set the water level to 3 again and go down onto the second level of the mine. There's another fenced off area here; go in. After swimming down a long series of shafts you'll come out in the place where you found the Air Necklace. Climb the wall here to find a dragon.
Unicorn: use Rouge in Dry Lagoon. The first Chao box is forward and to your right, in a little corner nook. Climb the wall and look in the same corner at the top of the area for the second box. Go back down and ride the turtle to the other half of the level. Directly in front of you is a stone circle; stand in the center of it and whistle to get the hidden unicorn. Then get up on the left hand ledge and climb up the pillars; on top of one is the third Chao box for another unicorn.
Phoenix: there is probably a better way of doing this, but I just get the three Chao boxes in Rouge's Security Hall. From the start, run forward following the rings, turn left and ascend the wall to get on the ledge with a spring. The spring takes you up to another ledge with a lifting cable; take the cable. At the top, climb the wall. You face an area with lasers; jump through the first two and turn to your right behind the block to find the first Chao box. Now get out of there again and fly around the fence to the right hand side of this room; go to the farthest end of it and fall down. There's a switch there; press it to unlock the blue safes. Climb up again and fly back round to the hole where you came up. Fall down it, and fly to the right, towards the corner where you started. Make sure you land on the level where the safes are blue. Open the safe in the very corner for the second Chao box. Now fly out and turn left; fly around the jutting-out central area and land on the ground on the right side of the fence. In an alcove here is the third Chao box with a phoenix. It all sounds complicated but once you've got it in your head you can do it fast.
Black type:
For skeleton dog and bat, use Knuckles in Pumpkin Hill.
From the start, go forward and take the left-hand route for a rocket that will put you on the top of Church Mountain. A skeleton dog is walking around the gravestones here.
Fly over to Train Mountain and, from the top, step out onto the jutting-out platform without a switch and fall down onto the platform you see below on the left. Two piled wooden boxes hide a bat or skeleton dog.
Climb up to the top of the mountain again and glide to the balloons you see, popping each one. That will get you to a pumpkin island with a tank on top; kill it or not, but climb down the stalk of the island. At the back is a ledge with the first Chao box. Glide back towards Train Mountain but go straight past it; you'll see a network of platforms in midair. On the right-hand one of these is the second Chao box, with skeleton dogs and bats aplenty.
Back at Church Mountain, go around the side of the mountain a little way from the top, and you'll see a switch with a rocket; when you press the switch, the rocket blows up a cage, freeing a bat for you to get.
Fly over to Pumpkin Mountain. The third Chao box is on a ledge around halfway up the mountain; it's easy to spot. It will contain a half fish as an added bonus.
Still on Pumpkin Mountain, climb on the wall and climb left and down from where you found the third Chao box. There's another narrow ledge with some train tracks; on a little raised platform you'll find a bat.
For half-fish, use Rouge in Egg Quarters.
Turn left at the start and run around to come out in a large room. This can be tricky. Go past the central platform and look along the right hand side near the far door. There's a half-fish in a cage. Getting it out involves a tricky feat. On one of the nearby pillars there is a Coconuts. Stand around 1/3 of the way out from his pillar, facing towards the cage; he will throw a bomb. You have to pick it up and throw it towards the cage before it explodes. An occasional roving scarab further complicates matters. If you manage it, the half-fish will be freed.
If you want to go for the boxed half-fish too, start in the blue room and hit a rocket switch to blast away the grille in front of the central door. In the room beyond, the Chao box is to your right underneath a regular brown box. You get the second Chao box by playing the mystic melody on the central pillar in the room with the caged half-fish. An E-100 is standing in an alcove, guarding the box. The third Chao box is found by continuing on from the cage room; you'll find it on your route.