I vote for Crystalis, one of my favourite RPGs ever. Faxanadu is also a favourite of mine (anything RPG + platformer is, really), but it has descendants in other forms & I've never seen another game quite like Crystalis. Basically the same thing again but with better graphics, slightly longer quest, & more character interaction.
I'm not sure how I would feel about a Mega Man on the PCE, because I really haven't cared for any of the nextgen graphics Capcom's come up with for the series. But Contra would have rocked (would have been a perfect fit, I think) and I would totally love a Dragon Quest title with just slightly more detailed graphics. That, to my mind, would be perfect.