Dominions II maps work in Dominions 3. There is at least one glitch (#seaplayers 0 not preventing random nations that start underwater), but this isn't major and probably not limited to DomII maps. However, the fact that Dominions now supports alpha channels can cause some problems.
Parganos (at least version 2 by Ironhawk), The Three Necks, Karan and who knows how many other DomII maps just won't show up in Dominions 3.
Daynarr has posted how to fix the alpha Channels in
Gimp. EDIT: Please note that this is inside the bug thread. It's not a very good bug thread, but it'd be better if we at least tried to keep it just for bug-related issues.
Are there any other programs with which this would be easier to do? Gimp may be free, but it's cumbersome to install...