the main reason disgaea 3 is up there for me is because it played exactly like the ps3 version, except it includes all of the dlc, some extra content, and some gameplay tweaks to make it better. AKA it's an enhanced port with all of the dlc for less than the dlc costs on the sp3.
as for MK, I don't play fighters online so online play being limited for me doesn't matter at all. My thoughts on that is just because it's a well made port with tons of offline content including a whole new second Challenger tower. the fighting isn't quite as pretty as the ps3 version, but it still feels just like the ps3 version with no cuts in framerate.
As for ninja gaiden I honestly haven't played a lot of it, and it looked good, but to my understanding it has major frame rate issues from time to time and doesn't really have much in the way of new content. I've heard it's a solid hand held version, but in general it's inferior to the original version which to me doesn't make for a great port. A good port should improve upon the original, not just get close to meeting the original's standards (which some would argue that given it's half frame rate that it doesn't even get close to meeting the original's standards)
It's why persona 4 is up there for me as well, as not only is it a great game in general, it looks a lot nicer on the vita, and the gameplay changes really are solid. It did nothing but improve upon an already great game which as I said is what i feel is what really makes a good port.
my list will likely change quite a bit later this year though as there is a high chance that the binding of isaac will drop persona 4 down to the runner up for best port for me lol.
i haven't a clue if this was mentioned yet but... "
Cloudberry Kingdom confirmed for PS3, Vita, Wi U, XBLA and Steam this spring "