About one month I switched from using Vorbis ripped with CDex to Monkey´s Audio ripped with EAC. First I was very disappointed that EAC could not write APE-Tags to my apes automatically, but then found wapet and it worked fine. But still I had to run replaygain with foobar.
I thought that this can be done by wapet, it writes the tags, why shouldn´t it write the replaygain info in the tag, too? OK, but where does it get the replaygain info from? First idea was to decode the encoded file again, calculate the replaygain and tag the file. But why to decode it again? EAC creates a temp file which will be identical to my new decoded file, since monkey´s audio is lossless. So I yust I implemented a simple wav parser and the replaygain analysis into wapet, which calculates the replaygain from the original wav faster than foobar does from the ape. But only radio gain is supported.

Usage is simple:
Without replaygain (yust normal):
With replaygain:

This patched version with sourcecode is attached. I can´t really code C, so code looks not very good, maybe Case can clean it up and make an official release from it. I hope for someone else this is as usefull as for me.

This might not help you with replay gain, but EAC works nicely with macdll.dll. Rips and converts to monkey's audio with tags and all, in one step.