You can always dump it back to wav, fix the errors with Soundforge or something, and then re-encode it, but of course you lose some clarity that way. It is not that hard to find the pops and clicks and fix them (finding is usually harder than fixing), I do it all the time when I rip dirty CDs.

Of course some CDs are so bad that it isn't worth the time to do all of them. When that happened I usually got a copy some *cough* other way. Thankfully almost everything I rip nowadays are new CDs. If you are going to re-rip them I suggest Exact Audio Copy, it has ripped some CDs I thought unrippable.