TBH, if you look at the service schedule for 30K miles, and do everything it says, you won't be far off. Do all the usual stuff as RBJ says, but there are a few notable things that are worth doing in addition to what the book says:
Forks, for example, aren't mentioned as a specific item to service. Trust me, they'll need attention at 30K, if nothing else other than a flush and fresh oil. But if you take them out, for the minimal investment a strip and new seals will make sure things go the distance.
Re-sealing the airbox side covers is a good thing to do that isn't mentioned, particularly if (like you) the bike is used in dusty conditions.
Cleaning out the gauze strainer at the base of the oil tank (frame down tube) which is part of the oil pipe union is worth doing. Again not mentioned and often overlooked.
When you service the swingarm/linkage, get rid of the solid MPL lubricant and replace with grease. My bearings were looking sad after 12K with the OE MPL, but after pulling it all out and replacing with waterproof grease, at 24K they looked mint. Same mileage, same riding conditions.
See these threads by Ohlins for a walkthrough:
Part 4:
http://www.xt660.com/showthread.php?t=20738
Part 3:
http://www.xt660.com/showthread.php?t=20737
Part 2:
http://www.xt660.com/showthread.php?t=20736
Part 1:
http://www.xt660.com/showthread.php?t=20735
After 4 years the brake lines should really have been replaced, which although in the service schedule is often overlooked (by DIYers and dealers alike). They will have sufficiently degraded enough at this age to be leaving rubber particles in the fluid, even after you change it and will be have more "give" under pressure than new.
Check all the wiring, not just the reg/rec connector, especially where exposed and clean/lubricate any connectors. Also check for abrasion, especially under the tank where the injector spur off the main loom is known to wear through. I loosen all the cable ties and inserted foam pads early on and everything is goo still.
Check the top hose where it runs round the back of the cylinder head. I found at 12K that the hose was rubbing through on the bolt heads that hold the inlet valve inspection covers in place.
There are probably other things too, these are just some of the extra jobs I did on mine.