Hey Spriter's Resource. My team loves pixel art and our first game, 100 Rogues, was 100% pixel art. We want to do nothing but pixel art, but because the platform we're targeting next (Android) has many different screen resolutions, we can't come up with a good solution. Here's a blog post we posted explaining the problem in detail.
http://www.dinofarmgames.com/?p=262
What do you guys think?
This actually shouldn't be too much of an issue; the biggest problem would have to be how into using the same general resolution you are for all of your projects. You shouldn't really worry about compensating by making the resolution a little larger/smaller based on the platform, while still keeping the pixel art at its normal scale. This just gives you more (or less) space to put content in.
An example; using the same size sprites for a 320x240 project as a 480x320. Keep the sprites at their normal scale; on the 480 version, you can fit more sprites in than the 320 version but still provide the same general gameplay experience.
That might be a bad example but it should at least give you a general idea. For stuff of the larger res, just blow the sprites up to a precise size (200%, 400%, etc).
Hope this at least helps you get a springboard of what to do, at least.