Depends on what you mean by "libraries". Flixel and FlashPunk are basically Game-Engines and have implementations for collision-detection, particles, animation, save-games, audio playback etc.
Other than these two you mentioned, there's also the Push Button Engine which is more modular than the other two.
If you're interested in learning Flixel or FlashPunk, you should have a look at their collaborative Website Flash Game Dojo which is a good resource for Actionscript based games (especially if you're developing with Flixel or FlashPunk).
There are several specialized libraries that are very useful for flash game-developers too:
- Polygonal Datastructures implementations of several commonly used data-structures. Optimized for speed.
- Turbosignals a signal/slot implementation that's optimized for speed. Very useful for games and a great replacement for flash events.
- ... and of course libraries like Away3D or TweenLite