Most everything should be in the owner's manual but I would check the following:
Valve check is due if it hasn't been done
Do spark plugs and coolant change at the same time
Do throttle body sync afterward
Bleed brakes and clutch - fresh DOT4
Clean and lube rear brake pivot and brake lever.
Check brake pads and you might want to clean up calipers.
Change fork oil if it hasn't been done lately
Check air filter
Change rear drive fluid
Might want to check/clean/lube U-joint and drive splines
Definitely check/clean/lube relay arm
Check/lube/retorque steering head
Visual check of ground "spiders"
Check with Yamaha on recalls - there was one for the S4 "spider" and one (I think) for the ignition switch
Can't think of anything else, offhand. That should get you going...
Oh, There was an issue with problem cam chain tensioners with the '06 and some '07. I think it was cleared up by '08 but check to see if your CCT has a blue or green dot on the side... If not (or you can't see it well enough) it might need to be replaced.
Edit: The above is applicable to all FJRs. For the non-AE version, I would add regular servicing of the clutch lever and shift linkage. The clutch lever, in particular, needs to have the brass bushing that pushes in the actuator cleaned and greased along with the pivot. Once per year (or more if you ride in a lot of wet) for brake pivot, shift linkage, brake and clutch levers.