A couple come to mind, altho I have to say I have experience of neither but have heard they are both very good solutions:
Pro Motion: This commercial package has been around for some time, and is the choice of many professional commercial 2d game artists. It has many features including the ability to export to many proprietary graphics formats, as well as advanced animation tools like onion skinning (overlaying animation frames, classic technique)
There's also a cheaper Lite version and a trial version available for free download.
Interestingly enough, they are also planning to release a sub-pixel anti-aliasing plugin for Photoshop,
Pixus, that aims to make graphics much clearer on small handheld screens.
A completely different tool that is perfect for creating isometric "pixel art" is
Caligari Truespace. It's an old 3d tool that is now free, and I've seen some impressive iso work done with it, like over at the excellent free game graphics archive of
Reiner's Tilesets.
Good luck!