Too many long posts here, so back on topic :
actually, my favourite pce fighting games are not ports. Why? Just because when you play fighting game ports, they feel like they are ports. I mean, Fatal Fury Special is a very great port indeed but some of the backgrounds are not very nice (Andy Bogart's stage, for instance) while others are really well made and are really close to the original (Tung Fu Rue's stage is the most impressive to me). In a way, World Heroes 2 is the best Neogeo port for the PCE as it is the closest to the Neogeo version of the 4 Neogeo ports. Too bad it is a port of a Neogeo average game, even if I like it, though.
So here is my list :
1) Kabuki Itouryoudan : great graphics, great animation, smooth gameplay and you really feel it was developed exclusively for the PCE, as the backgrounds are not overdetailed as some backgrounds in FF Special.
2) Flash Hiders : many people I know don't like it. Some backgrounds I really poor graphic wise but I like the gameplay, the sounds and the animation.
3) Fatal Fury Special : great port. I enjoy playing this game even if I own the Neogeo version.
4) World Heroes 2 : the best Neogeo port on the system, in my opinion
5) Asuka : decent fighting game
I also kinda like Godzilla. It's really different from the usual fighting games but I think it is the best game based on the Godzilla characters of all times (not too hard).