I just used Quicktime Pro 6 -- it provided excellent image quality and the .mov could be imported to After Effects. Unfortunately I no longer have it because I need to watch Quicktime 7 movies and you can't install Pro 6 and Free 7 on the same computer. Stupid Steve Jobs.

Also if you have an AlphaChannel in your images (Targas) and you save the movie as "millions of colors+" you get the alpha channel with it (that's what the plus sign means). Which means -- you can composit your layers perfectly being that Maya does the "keying out" automatically for you.

It'll also be helpful if you wish to save your movies as h.264 -- but being that I only used Pro 6 I don't know how to do that. (That's a 7+ feature)

I think you click File -> Import Image Sequence and click the first frame (assuming they're numbered -- else you need to add them all in order by hand), but its been a while.