Personally, I am not a fan of anything that repairs clicks and pops automatically. I prefer to remove really noticeable clicks and pops individually and by ear in Adobe Soundbooth, then let well enough alone. The really bad ones stand out visually and aren't hard to spot once you know what you are looking for.
Amadeus Pro has a nice tool that seeks out cracks and lets you decide whether to repair them individually, and this can save time. But the results are not as good as the click removal and auto heal tools in Soundbooth. Click Repair has an option to let you accept or reject repairs manually, but you don't get to hear them in context as you can in Amadeus or Soundbooth.
Click Repair is a really powerful program, but it has it's limits. When I first tried it I was amazed at how much noise it was scrubbing out of my LP recordings. I had no idea my records were so noisy! And certainly when I listened to the noise output, everything the program was repairing sounded like surface noise. Then I noticed that the resulting files sounded strangely lifeless. Out of curiosity I ran some CD tracks through with the wavelet filter at the LP default of 50. The result? CR "repaired" nearly 14,000 separate "clicks" on a 3:00 CD track. Reducing the sensitivity will give less aggressive results, but it also increases the chances of leaving actual clicks in.
Separating clicks from music is a really computationally difficult task. Differentiating a hand clap or snare crack from a pop or click can sometimes be difficult for the human ear, let alone for an algorithm. The author of CR is very upfront about these limitations and the impossibility of definitively distinguishing music from damage.
CR is a great tool for cleaning up really noisy recordings, but for an average LP in good condition, I find I get better results just taking out the worst clicks and pops by ear and not fretting too much about noise that is inaudible behind the music.
Any method of click removal involves trade offs. Doing it by ear takes a long time, but in my experience it gives the best results. I do recommend trying the demo of Click Repair, because for cleaning up really noisy recordings it is great. Your mileage may vary, etc.