If you're coming from 3.5, you won't notice the "slowdown" that people often rue about 3.9, since the speed of the reaction user interface (which is considerably slower than gadtools, but that's the price you pay for a resizable interface) is something you'll already be accustom to.
There are various tricks to squeezing more out of it, but in all honesty, I've not bothered on my 3.9 install. It runs just fine on my 040+RTG, as did 3.5. I can certainly confirm 3.0/3.1 are snappier but I doubt I'd ever go back to them for my everyday Amiga fix (I do boot them to test out stuff, but that's it).
