Meaning "good" or "very":
* Very: very well
* Extremely: extremely well
* Perfectly: perfectly well
* Wonderfully: wonderfully well
Meaning "not":
* Not: not well
* Ill: ill-well (archaic, meaning unhealthy)
Meaning "to make or become":
* Well-: well-being, well-bred, well-intentioned
Meaning "a source of water":
* Artesian: artesian well
* Oil: oil well
* Gas: gas well
Other prefixes:
* Deep: deep well
* Shallow: shallow well
* Dry: dry well
* Wishing: wishing well
The best prefix to use depends on the context and the meaning you want to convey.