I've come up with a list of possible in-game moments and some overall music needs for games.
It all depends on the content, really. Without knowing how the game breaks down, I cannot really say if your list of proposed cues would work or not. This is more something you'd figure out along with the dev team.
While programming this in-game, do/can game developers just loop .wav files and can pick and choose, with-out glitches? Would it be better to Fade out and Fade in for transitions...like you said,
It all depends on the tech that's being used. Many decent tools, especially the 3rd party tools, can definitely toggle between tracks based on gameplay data.
One more thing...what about naming and sorting all these music files? Does anyone have any preferences?
Again, it all depends on the tech used. Naming a file isn't as important if you're working with, say for example FMOD, but definitely play a huge factor if you're working in XML or ActionScript. The reason why is FMOD enables you to drag and drop in the audio asset then set the parameters. Something like XML requires you to type in the file name so the more complex/longer you make it the more likely typos can break the code.
It also depends on if you're the only person touching the audio files or if you're working with a crew of folks. When by yourself, it's much easier to set up a system and know what is what. But when working with a crew it's important to establish a norm that everyone can understand and follow - especially when crunching!