What is the best way to clean up after tweens in AS3 no matter what library you are using (or the built-in tween classes). Is there a best-practice or is it specific to each tween library?
If with "clean up" you mean to clean up the memory used for animations in flash, try
System.gc();
to fire the garbage collection. It will sweep everything out what is not used or lost its reference.
Recycling is also a good idea, even though it highly depends on your coding style and actual project.
For more information on the garbage collection, see the reference.