the result of pixen work can be one of:
-single image
-single animation
-character animation spritesheet

i think the least one needs a bit of rethinking.
it would be nice to pack few animations into a spritesheet of fixed dimensions (usually power of 2... 128x128 256x256...) and have the frames grouped by animation.
I like how this has been done in sprite something for iOS
http://www.youtube.com/watch?v=4_ZBI7KSI0M&feature=relmfu
basically you work on a big png and see a portion of it (the frame) then you makes animation by chosing sprites from the big sprite sheet.