Well I'm not sure about the animated enemies (I assume you're using the built-in battle system), but, as for the bigger heroes, you can use Battle 2 anims. These are pretty much like normal battle animations, except they're 640 by 640 pixels in size (and still 5 collums with 5 cells each, each cell being sized 128 by 128).
Import these like any other resource (folder is 'Battle 2'), then go to "Database > Animation 2 > Animation Type". See each possible 'stance' in the list right below? Mark the box on the right of each stance for 'Battle Animation' (they're set, by standard, for 'Character Pose'). You can, likewise, add new poses in the "Database > Animation 2 > Poses" menu.
...'Kay?
P.S: About these animated enemies! Check this video:
http://www.youtube.com/watch?v=6hKMdfwqFo4 . It shows both animated boss and extended hero animations. I think I know how it was done, but it's rather time-consuming. Which is why there are so few complete RM2K3 games using this system. You might want to check out Phantasia III (
http://www.kobrasrealm.net/viewgame.php?12)