Tag&Rename is capable of writing APEv2 tags to Monkey's Audio files.
QUOTE
Support for: mp3 (ID3v1, ID3v2.2, ID3v2.3 and ID3v2.4 tags), MusePack mpc/mp+ (APEv1, APEv2 and ID3v1 tags), Windows Media wma, asf and wmv files, Ogg Vorbis and Flac (vorbis comments), Apple iTunes and iPod aac (m4a) files including mp4, lossless m4a and protected m4p files, most popular lossless codecs including monkey’s audio, wav pack, optim frog, flac, Apple and Windows Media lossless.
It imports meta-data from freedb and Amazon.com.
Unfortunately All Music Guide is no longer supported due to AMG's site change.
The GodFatherWhich supports .mp3, .ogg, .mpc, .ape, .flac, .aac, .apl and .wv files.
And does quite a bit, not to mention it's free.
Hope this helps, tec