I've used Flac for awhile now and have archived my CD collection with it as well but the other day I ran into something that I never had with it and need to know if there is a remedy. I downloaded some Flac files where the songs were already broken up into individual tracks but it also included the cuesheet. Now the problem is that on some of the files there are gaps between songs on albums I know there shouldn't be. And I've converted to Wav and even burned onto a CD using Disc-at-once but there are still gaps between some tracks which I know aren't supposed to be there. I figure that the Cuesheet contains the information telling the player or the burning program where there should be gaps on an album and where there shouldn't be, so my question is how do I implement the Cuesheet if that is indeed what it does?

Try playing back the cuesheet with foobar2000, if it's a compliant one it should work, otherwise you'd have to hunt for an 0.8.x version of foobar for non-compliant sheets. But I doubt that it works, the FLAC files should play gaplessly as is, usign a cuesheet won't delete the gaps, probably just introduce new.

Get CueTools 2.0.2, first join the files, then split them again (using new .cue) with gaps left out option.
If that fails, edit cuesheet (see HA Wiki), and you can always trim the tracks manually, w/ audacity or something similar.