I personally couldn't live without DOpus5.82 (in WB replacement mode). Very highly recommended.
Adds power and configurability like never before.
I personally found DOpus to be a far more significant upgrade, than the shift from 3.1 to 3.5 was.
I looked into uprgrading to 3.9 (from 3.5) and decided it wasn't worth it, for me anyway.
Many of the new features it provides can be got through various stuff on Aminet anyway (Some like XAD and MooVid need to registered though).
However IIRC 3.9 contains much better options for Web browser and TCP stack than did 3.5 (it's TCP was a time limited demo!). So if you don't already have IBrowse and Miami or something similar then 3.9 would definitely be a better option than 3.5.