I'm very happy with ClickRepair. All it does is remove ticks, pops, and crackle, it's not a general noise reduction tool.
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Sony Sound Forge Pro, at $375, is a professionally oriented Windows-based audio editing program which includes several functions that will reduce or eliminate tics, pops, crackles, rumble, and continuous surface noise.
I have used this program extensively, but not for those purposes. Once you get through a modest learning curve, it is fast, easy to use, stable, and powerful. The particular functions you would be using have a lot of flexibility in their settings that allow you to optimize the trade off of noise reduction vs. possible side effects. The program will not work miracles, but should allow you to improve your copies significantly.
They also offer a much cheaper consumer grade program which you will see on their website, but I don't think it includes the functions you would need.
The program was developed by a USA company named Sonic Foundry, btw, which was bought by Sony a few years ago.
Check out Audacity http://audacity.sourceforge.net/. It's a really nice sound editor with click (and other noise) removal and it's FREE! Depending on your setup, it can also record from the line in on your sound card and then split and save the tracks (although this will be a manual process).
These methods will all work to remove noise. If the noise is REALLY bad, not just some random clicks but really bad surface noise, the filtering can be somewhat destructive to the audio. So you have to use the filters carefully.
The challenge you have is that you have copies in 16/44.1
(redbook) and you basically need to:
1. Copy the CD's to your computer
2. Run them through click repair (which I use to great success) or another piece of software
3. Burn them back to CD
I prefer to do the rip and edit as 24/96 files ripped to my Mac. Then, do the edits/filters, then down-convert to redbook if I'm going to burn a CD (which isn't often these days).