Software can remove noise, but really it's not going to help. The problem isn't noise (hissing or humming), but compression.
The GF soundtrack was compressed a lot so it would fit onto two CDs (Imagine how many CDs it'd take if it were all the same quality as the official soundtrack CD!). Unfortunately, compression is a one-way thing: once that data is gone, it's lost forever. The only way to retreieve it is to get hold of the files before
they were compressed -- or in other words, before they were ever put on the game CDs.
As nobody outside of LucasArts has access to those original master copies there's not much we can do.
It all depends on your audio equipment, of course. If you're not listening to the Grim Fandango music through high-fidelity speakers and amplifiers, chances are you won't notice the quality difference. High-fidelity stuff really brings out the compression though, and you can hear the sound being distorted.
I suppose the best comparison is to a video on something like YouTube. Once YouTube compresses it into a Flash video, the quality is gone forever. You'd need the original video from the author before he uploaded it to get the high-definition stuff.