I use both, but when I can choose, I go for chipmunk, it has much better API, and was much easier to learn...
But that was because I learned it without need for a community, the manual is completly fine.
UPDATE: My current game is using Box2D, and I wish I used Chipmunk with it... Mostly because Box2D has two serious issues, that are exacerbated on my game: First, it has a REALLY OLD bug where objects "snag" on corners, my game is a breakout game, so when the ball is "rolling" along a wall, sometimes it snag and is flung away from the wall, lots of people asked why my game physics looks "random".
The other issues that Box2D have, is how it store objects, Chipmunk use a spatial hash, and Box2D use a binary tree, my game was having MASSIVE slowdowns in levels with lots of objects, I asked Erin (author of Box2D) the reason, and he explained that because Box2D uses binary tree, if you place objects in a grid (like I said, my game is a breakout clone! everything is in a grid!) the tree gets unbalanced, and Box2D slows down. The solution for my game was make some levels into a "checkerboard" pattern to avoid this problem.
So, for all tile-based games, I will just use Chipmunk, Box2D REALLY is unsuitable for those (because the "snag" on tile corner bug, and the slowdown bug with tile grid)
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