I've been using EAC for a good few months now with Accurate Rip. The settings I use in EAC are here. I set it up after reading the tutorial on The Coaster Factory.

I'm still getting clicks on some CDs that I rip, on CDs that are brand new and clean (not copy protected). They play fine in Windows Media and Accurate Rip is reporting that the rips were accurate. The clicks are in the same place each time, I've tried a few different audio players and other sound cards and the clicks are still there.

Any ideas?

Rip to Wave then see if the wave file has clicks.

I rip all my CDs using T&C > uncompressed.

Is there a better program I can use for ripping or is EAC the best?

I cannot answer that as I am biased

If accuraterip verifies the rip then:

The original has the clicks (as someone elses cd has the clicks),
Your cd drive has bugs, someone else has the same drive, and same CD (very low probabbility, even less if the confidence is high).
The data is changed after ripping (most likely), perhaps bad hard disc, encoder setup wrong.

Thanks Spoon! Now I just have a question about Accurate Rip.

I've just ripped a track from a CD to wave using secure T&C. The Accurate Rip results

Track Ripping Status [Disc ID: 001a6cd8-ba0c010e]

1 Accurately Ripped (confidence 4) [3fd415e6]

_______________________

All Tracks Accurately Ripped.

What does the "[3fd415e6]" part mean?

If EAC had no problems + Accuraterip has a good confidence there should be no clicks from ripping.
I often have brand new released recordings that have clicks in the master already. Sometimes you may be fooled cause it is a smacking around a voice or some noise in the recording enviroment. You need a good system to qualify this exaxtly.
Looking at the waveform in an editor may help also. There are really funny squared bits sometimes that really can´t have a natural origin.
So if you are sensitiv to these clicks like i think to be, much fun! You´ll find them not to seldom

Or you might have Glitch removal option checked in EAC which is actually introducing glitches.

The number in brackets is a CRC.

Glitch removal option?

Why aren't the CRCs in Accurate Rip the same as the ones returned in EAC?

Same here, glitch removal?

There are many different ways of calculating crcs, and by default EAC does not use silence samples in the calculation, AccurateRip does.

Did you try a standalone device yet?

No I haven't yet. Are they supposed to give better results?

So, the ''clicks'' are not in the original, and it's definitely glitches - not possibly clipping? Normalizing is disabled in EAC?

Try replaygaining the file, it may be clipping.

I've found that even if you do configure EAC to include silent samples in the caculation, the CRCs still don't match those calculated by AccurateRip. In addition, I have been able to get the exact same CRC of the raw PCM data using any program that generates a standard CRC32 checksum as what EAC displays.

No it's definately not clipping, normalizing is disabled in EAC.