Just took a look at the 3.9 install for my Apollo, which I spent quite a bit of time fine-tuning a few years back.
One annoying thing with this card is that exec.library always ends up in chipram, which isn't optimal and slows things down a bit. You can get around this by using MuMove4k and MuFastZero from the
MMULib archive, and/or using Piru's exec44 loaded via
RemApollo. The nice thing about RemApollo is that it's compatible with some of the excellent
BlizKick modules. SpeedyIDE is useful if you're not using Doobrey's scsi.device or IDEFix. With my 80MHz Apollo, I was getting about 5 MB/s raw read with an IDE-Fix express, better than most '030 cards which are usually fastest due to better chipset access.
You can also use RemApollo to load some updated OS components (like Doobrey's patched scsi.device), or use ROMSplit and Remus to compile your own custom ROM with everything already added, then re-kick the ROM image with RemApollo, or burn it. And don't forget about TLSFmem.
Ultimately, if you're like me you can spend most of your time on the Amiga tweaking and benchmarking the OS, without actually using it to run programs or do anything useful. :-o
-edit- Though not strictly related to the Apollo, Peter Keunecke's
icon library is an absolute must-have IMHO. Speeds up icon loading tremendously, not to mention a ton of other great features.