If your original CDs had scratches on them, rippers will sometimes try to compensate for the missing data by inserting a chunk of data to fill the gap so that your music doesn't skip forward, losing the beat. This generates that "squeaky click" sound. This may or may not be your problem. The easiest way to find out is to do a controlled experiment:
1. Pick one track that seems to exhibit the problem frequently
2. Play this track on several players, noting the times within the track that you hear the clicks.
3. If the clicks happen at the same point in all players, then most likely you've got an MP3 with some corrupt/missing data. See my comment about scratches above.
4. If the clicks seem to be happening at random, then you might be having some kind of hardware problem. A hard drive/CD-ROM set in PIO mode (instead of DMA) will often cause MP3 playback to skip due to the system blocking on disk I/O. Also, electrical noise can sometimes infiltrate cheap onboard sound cards (and some expensive PCI cards too) and cause ground-loop hums, clicks, whines, etc. Not much you can do about that kind of problem. Finally, you could have something as simple as a loose speaker connection. A dirty/loose 1/8" stereo plug can make clicking/scratching sounds in your speakers.
I suppose that would just about cover the possibilities...start investigating!
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