If you get glitches in ripped tracks (whether AAC or MP3 or WAV, etc.) that usually indicates that the CD drive is imperfectly reading the audio data. To overcome this problem, do the following:
1. Make sure that the CDs are clean and free of (significant) scratches. A regular audio player can use on-the-fly error correction to "fudge" the scratches so you won't notice the data loss, but when ripping audio to a file it must be exact. A clean CD is a great place to start. Always clean them with a soft cloth, wiping radially from the inside of the disk to the outside.
2. Under iTunes preferences -> Advanced -> Importing, check the box labeled "Use error correction". This forces iTunes to slow down and retry areas of the CD where the data is not clearly read. This often takes care of things, I recommend that it ALWAYS be left ON. It WILL slow down the ripping process, but it is worth it.
If a CD is badly scratched, you may have to resort to more extreme efforts. Mild abrasives are available to buff out the scratches, but if the damage extends to the CD's foil layer you are out of luck and the disk is dead.
Finally, you may resort to an advanced, error-correcting rip program such as Exact Audio Copy. EAC uses massive re-read and error correction technology, and can port data directly to iTunes via some simple extensions.
http://www.exactaudiocopy.de/
Note: EAC is very geeky and not recommended for non-technical users. I have personally found it to be an invaluable tool for recovering damaged CDs. As a side benefit, it can read right through the pesky (buggy, dangerous) copy protection scheme used by Sony and thus allows you to use their CDs normally to rip tracks and play them on your iPod.
