I have the Clymer manual andI find the Clymer, along with sites like
http://www.klr650.marknet.us/,
http://www.multisurfacemotorcycling.com/
provides really good info. The factory manual (a friend here got it on CD, base manual and the 650 supplemental manual) is good if you are enough of a mechanic to know the stuff they assume you know (which I don't!).
Depends on your mechanical skills/level of understanding.
I'm in management so I basically incompetent to DO anything, except give advice!