These days most games that come out across multiple platforms have relatively minor variations; such as more resolution or a higher frame rate on one platform or perhaps a tiny bit more content tied to some exclusive deal. But back in the day games released on different systems were usually coded from the ground up for those systems and so had more significant differences. That often meant that some versions of games were notably inferior to others (2600 Pac-Man is one of the most infamous examples) but they were sometimes different in ways where someone might prefer the "inferior" version to another. The most common reason for this is, of course, because the inferior version is the one you had so it's the one you're nostalgic for. Sometimes there are other reasons why an inferior version might seem better for some people (like horizontal shooters that had slowdown but were slightly easier for that reason.)
The reason I bring this up is because you see a lot of 'collectors' excitedly going after old games where there are better options easily and cheaply available. People are excited to get Coleco Vision Donkey Kong even though a nearly arcade perfect version is available on the Switch. Or people who list Donkey Kong Country GBA as one of their faves even though it's washed out and screen crunched. What I'm saying is that there are a lot of people out there who love subpar Donkeys Kong.
I have two major choices:
The first is Gradius on the NES. It's actually a very good conversion but it's slightly worse graphically and sonically than the arcade. There are some other differences too, such as the Konami code existing in the NES version and the arcade version being generous with power ups after a death, but even though the Arcade version looks better and sounds better all my nostalgia is for the NES version. I have both available on my Switch and I play NES over Arcade. When I was a kid I didn't even know there WAS an arcade version.
My second is Gauntlet for the NES. It's not nearly as good as the arcade in basically any way but I had it as a kid and it has nostalgia value. I don't really like arcade Gauntlet and I probably wouldn't like the NES version if I hadn't played so much when I was young. But if I want to play Gauntlet that's the version I'd like to play.
So what are your favorite "I know there are better versions available but this is the version I love the most" game?
NOTE: I am not talking about "Same name, different game" situations. A lot of people like NES Strider more than Arcade/Genesis Strider, but that's just a different game, not really an inferior version. The same could be said for Bionic Commando, which is a better game on NES but is also just a different game. Contra is a more common example where they really are the same game but the more technologically advanced arcade version's vertical orientation and washed out colors make many people prefer the NES.