OMG! Awesome, Moitah. Another useful tools from you.
Ever since the new cue sheet handling was introduced in the foobar2000 v0.9 betas, I wasn't able to listen to all my "non-conpliant" rips if I hadn't sticked to beta 6. I made a thread a few months ago in the fb2k sub-forums with no positive outcome at all. So I kept using beta 6, instead of abandoning my music and using newer betas (I didn't want to re-rip ~80 CDs or worse burn the backups to CD-RWs). And because I didn't want to miss the new features of 0.9 either, I didn't switch back to 0.8.3. That's over now!

Hey, now you got yourself another (beta) tester here.

I did a quick test with two CDs and it got me identical results.
First I tested one of my non-compliant rips (no pre-gap before track 1 tho): made a new cue sheet with CUETools, made a single wav with fb2k and one with WAVTools, then I enqueued all three "rips" into foobar and used the bit-compare tool to verify single tracks. No errors.
Then I ripped a CD to single tracks with a non-compliant cue sheet, and basically did the same as above, result was
almost no errors (see below for that). Then I ripped it again to a single file with a compliant cue sheet and did some bit compares again, also
almost 
no errors. (so EAC's secure rip proofed to be working too of course - the CD has some bad "spots"). Ok, the only problem was that CDs longer than one hour had wrong indexes (INDEX 00 63:24:44 --> INDEX 00 03:24:44) which you already
edit: fixed while I was writing this post

...but apart from that (and the FILE "Range.wav" WAVE) both CUETools and EAC's cue sheets were identical.
So far it looks good to me. Of course it were only two CDs (without pre-gaps before the first track...), but I'm sure if there is a problem with a special CD someone will find it.
Oh and I already got some suggestions:
- why not merge "WAVTools" and "CUETools"?
- add "batch mode"
- optionally delete old WAV tracks (in case WAVTools gets integrated)
and if you really feel like it:
- support for CLI de-/encoders
- and maybe even someone wants to convert single image cues to non-compliant ones, hehe
although that is already possible by mounting the image/cue - add support for converting multi-track EAC logs to single track logs, complete with CRC recalculation for the joined wav image
really j/k here
Well, thanks a lot for this tool! (It's the small things that can make people happy.)