Before you flatten your image, while you're looking at a chunk of image floating on a transparent background (image on another layer, the Background Layer transparent - little checkerboard pattern), just do this:

File>Save As> choose PNG and Preserve Traqnsparency which I've found works best - GIF is gonna compress the crap out of your image (if this is for web, it can be okay if it's teeny).

To save as a PNG, you don't have to flatten it at all - PS will save it as a copy of your doc, and it will be flattened and the background wil be transparent.

Hope this helps-
-Lew ;-)