if you haven't read the wonderful links those Mods brought up, I'll sum it up for you...
Certain Addon WADS (namely Duke Nukem and Half-Life and StarWars) All are modded somehow to a point that Rockdoom cannot play it (although I can't remember exactly which Doom port Rockdoom is made from, I do remember it's rather basic). These other WADS either have HUGE sprites (from giant title screens, to weapon sprites that are just BARELY over the size limit), and/or DECORATE or other type modifications that change the gameplay of the game (like Action Doom, or the Doom III weapon Mod)
Some of those WADS were ment to be played in Zdoom, or another port (or iDoom, if you want to try IPL. it can play most any wad, but it's a bit of a pain, no sound, and can't change control scheme. but still cool), but as for Rockdoom, it can't.
that doesn't mean you can't try them anyway
. sprite changes (like Wolfendoom and the Doom 64 weapon mod) will most likely work. I test many wads on my ipod (with usual failure -.-), but it's still won't hurt to try. but if that "THIS WAD DOESN'T SUPPORT REGULAR DOOM GRAPHICS" popup comes up, it basically means that the addon won't work