Here are the top ones I've read about or have actually done:
1) Suspension Tuning - Depends on your weight, riding terrain, and riding style. Stock fork springs are good for 130-150lb riders, the rear spring is good for 170-200lbs riders. Don't know why it's so unbalanced right out of the crate. Had my forks done by MX-Tech. Still need to fine-tune the clickers and set sag.
2) Better Tires - Michelin S12s are popular here in the Michigan sand. Really makes a difference in the rear end hooking up and the tracking of the front end.
3) Steering Damper - People that use them swear they won't ride without one. Makes the bike safer, more controllable, with less rider fatigue. I have a WER on order. Will hopefully get it in and on the bike in time for a ride this weekend.
4) Air Box - Remove snorkle and drill a bunch of 1" holes in the top of the air box cover. Makes the bike breathe better. In most cases does not require re-jetting because the bike is a little rich to begin with.
5) Pre-Mix - Mobil One MX-2T at 40:1 is popular. I've used it without any problems, and zero spooge.
6) Bark Busters - If riding woods, get a set from Enduro Engineering, Fredette, or Moose. They are very good bars (all sourced from the same vendor - EE).
7) Stronger Handlebars - Renthal, Tag - whatever your flavor is. The CR-Hi Bend is close to stock. Get a 1-piece top clamp from Fredette so the bar doesn't twist as easily in the rubber bushings.
8) RB-Designs Carb Mod - Along with some Boysen reeds, gives you some very crisp, responsive throttle response - especially in the low-mid range.
9) Pipe - FMF is popular, but I've heard about a lot of fit and finish problems. ProCircuit will be my choice for mods this winter.
10) Skid Plate - I haven't found one that really wraps up around the water pump, but the Moose one does extend out along the little ear lobes that stick out at the bottom of the frame.
That should keep you busy for a while! :thumb:
...And don't forget the protective gear! You can't enjoy any of these great mods if you are laid-up with an injury! :scream: