A less famous Theme, even though it has made it into three games (as far as I know), is Bowser’s Theme from Super Mario Bros. 3. Even though, it is an interesting example how Game-Music can develop. I will show you three versions of that melody. (The embedded youtube-videos are not made by me and just found on youtube)
The first one comes from the original NES-Version of Super Mario Bros. 3. That game is one of the “late” NES-Games, as you can see when playing it – the gameplay is already much more fluent, the graphics are “smoother”, than in older games (like its predecessors Mario Bros. 1 and 2), but still, the sound is not much superior to GameBoy-Beeps.
Nintendo re-released Mario Bros. 1-3 a few years later in Super Mario All-Stars. That is, all the three Games in one cartridge, with better Graphics and better Sound. Therefore, there exists a second version of that melody. But actually I like the first one better, because – well, this is a very short theme, for a comparably short boss, which was made to consist of beeps. I dont think that it really fits in something better than that. Anyway, here is one video containing it – it also contains the faster version (when the time you have to beat bowser is running out):
The latest version I know comes from Super Mario RPG. There, Bowser is the first boss. So I think that is the reason why they didnt choose a more complex theme for that fight. It is not really an important part of the game. Anyway, this version is slightly better than the previous.