Oekaki.nl, a Dutch website, has a browser-based pixel art animation program called "Animaki". Don't dismiss it for being "just" an HTML5 app, because it's surprisingly complete - even more so now that version 2 is out.
A demo can be found here: www.oekaki.nl/animakidemo.html (no installation or plugins required, works in most browsers except IE).
The demo starts with a 64x64 canvas. If you need a different size, you can go here and use the form (in Dutch).