I don't have an 'Android reader application' myself, but some features that I find important in my e-Reader (Sony Reader PRS-650) are:

 - Ability to organize books into collections (or tagging could be a substitute)
 - Dictionary (double tap a word and look it up)
 - Ability to annotate/take notes
 - Ability to adjust zoom level, margin cuts, font sizes.
 - Brightness control.

The supported eBook formats is important as well.