I agree that the "nostalgia factor" can definitely be a big one for most folks. For me these days, when it comes to multiple ports of a game (Earthworm Jim is a perfect example), I tend to research all the differences and choose the option that I find most appealing. While the version of EW Jim that I grew up with was definitely the SNES port, detailed comparison in more recent years ended up converting me to the GEN version and now that's the one I almost exclusively jump to when I decide to play it.
The GBA ports of Super Mario World and Yoshi's Island are another good example. Honestly, I find Mario's added voice lines in GBA Mario World to almost entirely ruin the game for me. Call it nostalgia if you want but something just feels "wrong" about hearing Mario chime in every single time he grabs a power-up. It actually grates on my ears. I love you, Mario, but just shut up, huh? The same applies to GBA Link to the Past. I don't need/want to hear Link's "hyyaaaah" every time I swing his sword. So, I just don't play those ports.
So, for me, while I have an underlying tendency to prefer an original to a port in 90% of cases, these days, I evaluate them on a game-by-game basis.