Hiya,
Had a play with all of this last night.
Tried the MMU libs 060 (+mmu.library), seem to be stable but they also seemed to run Quake slower than than standard (patched) Apollo libs, also not sure how compatible it is with RemapApollo. I might still try to use them to create a 3.1 boot floppy to run some demos that don't seem to get on with my standard 3.9 setup.
I also built the exec v44.1 but it only comes as a 3.1 complete rom image (which you can't seem to split for some reason), this is no good for me because I'm running RemapApollo with 3.9 and patching the built in 3.1 rom image with the Boing bag updates (loaded as modules). I'm not even sure if it's such a great idea to run v44.1 exec.library if you are running 3.9.
I updated my CopyMem 060 patches to the faster version listed in this thread. This didn't effect the frame-rate in Quake though, even running without any memory copy patches doesn't seem to have any real-world effect?
Also tried Cosmos's updated Apollo 060 library, so far no problems with it and it's maybe a little bit quicker too.
Didn't try the updated memory allocation routines from Chris Hodges (also mentioned in this thread) because it seems that they are less useful if you are running 3.9 + bb2 (which has updated memory allocation code).