Far too many to list. These ports have completely different design goals.
Chocolate aims to be nearly exactly the same, in look and feel, to vanilla (that's the joke behind the name). So it will bug in the same way, crash in the same way, etc. The game resolution is 320x200 and no higher (any higher resolution will only work by scaling up the pixels). There are no new feature of any sort, except as compromises for getting the engine to run on more platforms (so it's only possible to bind buttons to actions such as "next weapon" or "previous weapon", which didn't actually exist in the original game, because some platforms don't have keyboards with the 1-2-3-etc. row of keys needed to select weapons normally; or it's possible to replace the MIDI music by external music pack because some platforms may not have a built-in MIDI player). Notably, there definitely isn't any sort of new editing features, and there won't ever be any sort of cosmetic enhancement.
GZDoom aims to be an enhanced port with more editing features and some cosmetic enhancements. You can change gameplay completely. Bugs are fixed instead of preserved. Sometimes behavior is changed if the original behavior is found to be wrong: for example in Strife, the corpses of enemies you killed eventually decay (normal corpses are replaced by gibbed corpses) and then eventually disappear entirely (gibbed corpses, whether they started this way or not, are removed). This also happens for "decorative" corpses (which are placed directly in the map editor), if it's something that is shared by a dead creature instead of a purely decorative sprite, then it'll disappear after a while; you can see that on the altar of the temple where you meet your first specter, there's normally a dead peasant on the altar but if you take your time getting there you won't see it. In ZDoom and therefore also GZDoom, this doesn't happen, corpses are persistent just like in Doom, Heretic, or Hexen.
If you want more details, you can look
and [url=http://doomwiki.org/wiki/Engine_bug]there for bugs you can get in Chocolate Strife but not in GZDoom; and
and [url=http://doomwiki.org/wiki/ZDoom]there for a quick overview of new ZDoom/GZDoom features.