murple: I installed 3.5 first, I did have some problems booting up at first because of the ROM update file (Amiga OS ROM Update) . I think OS3.9 has that fixed, but still get BoingBag 1 and 2 for OS3.9 ASAP. Also, make sure you have a boot disk handy, in case something doesn't work out.
That said, with WHDLoad you can get a large amount of old software to work, not everything perhaps, but a lot...
:-D