I would say these are the marquis ones currently, based on how badly they're camped:
Spawn of Onyxia
And if you include the time-dependent spawns, then also Restless Shadeling. The weather-dependent ones are very annoying to get, but that's more a matter of being in the right place at the right time and not as much due to competition.
As for genuinely rare, simply due to the very low number of spawns, then Snowshoe Hare is pretty difficult.
Or, if you want difficult to get due to pet battle mechanics, then Crimson Geode, because it likes to kill itself when it gets into trapping range.