Taking out all considerations of market value and collectability, I think the following ports are more enjoyable experiences than their corresponding PCBs, and if given a choice in which I could only have one of the two, I would in these cases choose the ports every time:
-Mushihimesama X360. The rapid fire options in the port are a big part of this, but the slowdown is also very accurate and the game looks gorgeous with the HD graphic overall. On the PCB you also cannot reset the high score table (through normal means), and some PCBs are bug-fixed while others aren't, which is annoying. I'll also add Matsuri Ver 1.5 here even though I have not played the PCB, simply because they removed the counterstop that made Maniac and Ultra modes uninspiring to play for score on the PCB.
-Espgaluda PS2 - Sprite flicker was removed, and the slowdown is very accurate. 240p output too!
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There are some games I find equally enjoyable on both port and PCB. Deathsmiles is a good example (because Arcade mode is nearly a carbon copy of the PCB version). Espgaluda 2 is another -- I think 360 mode in E2 is in some ways an improvement over the PCB, but I still really enjoy the PCB because it has a slightly different feel.
Anyone else want to share their opinions on this topic?