Modifications

1. Corbin seat. BMW is notorious for its uncomfortable seats, so I bought a Corbin seat. It's firm, it's heavy, it adds an extra inch of height, and it's wonderful. I don't slide forward when braking any more, and I move into the seat when accelerating instead of sliding backwards.
2. Touratech Zega panniers. Pannier brand selection is a religious issue. I chose Touratech because they were lighter than Jesse Luggage, and the removable lid makes them easy to open if you have gear affixed to them. However, you have to tinker with the Touratech Zegas to get them into a usable state. I had to coat the lids and interiors with sprayable truck bed liner (available at your local auto parts store) because the aluminum material oxidizes when anything touches it. You have to install the locks yourself which takes about 45 minutes. Get the removable bag liners; they are really handy.
3. Explorer Lite tankbag. I was reluctant to get a tank bag because I thought it would be bulky and interfere with steering. I chose the Explorer Lite from Wolfman Luggage and have been very happy with it. It does not interfere with my body or the handlebar controls. It's not the biggest tank bag on the block, but I like it that way.
4. Pelican topcase. I like small topcases because I think they look better and have less wind resistance. I bolted a waterproof Pelican 1400 to my top rack using machine bolts and a sandwich of metal and rubber fender washers. It works great.
5. FIAMM horn. I replaced the anemic stock BMW horn with a FIAMM horn from an auto parts store. I installed a new relay under the dashboard, and I used 12 AWG wire and a 10A fuse near the battery. The horn is grounded to an ignition coil and is installed using the original BMW horn bracket. It is not as loud as an air horn, but it is definitely more effective than the stock model.
6. Garage door opener. This is the best modification I have made to my bike! It is very convenient to push a button on the dashboard after a long ride and open the garage door without dismounting. I removed the circuit board from a spare garage door opener and wired it to the heated grips 12 volt line. That ensures the button on the dashboard works only when the ignition is turned on.
7. Works Performance shock. My OEM shock failed because of corrosion. Works Performance will build a custom shock based on your weight, gear, and type of riding. The folks at Horizons Unlimited recommend them. I have heard anecdotal evidence from several world travelers that Öhlins F650 shocks fail prematurely.
8. Heated grips. Once you use Hotgrips, you will never go back. If I could do it again, I would have chosen the variable knob version instead of the high-low switch for more granular control of the heat.
9. Touratech hand guards. These serve two purposes. First, they protect your hands and levers if you fall or are riding through brush. Second, they deflect cold air away from your hands while at speed. When used in conjunction with heated grips, your hands stay warm.
10. Hyperlites. These are very bright flashing LEDs that augment the stock tail light. Even if your tail light is covered with mud, these LEDs will still be visible. Hyperlites are easy to install and are a very important safety mechanism. If yours flicker faintly while your bike is idling, write to the manufacturer and ask for the extra capacitor that is compatible with the F650 charging system.
11. Radiator guard. The stock F650 doesn't come with a radiator guard. I bought one from Jesse Luggage. F650 GS owners can fabricate their own relatively cheaply using metal mesh.
12. Fuel bottle. USA models of the F650 have a carbon emissions canister that has a tendency to fall off, making room for other things in that location. I mounted an MSR fuel canister where the emissions canister used to be using the original mounting straps. It only provides an additional 10-12 miles of fuel, but it never hurts to be prepared. I stole this idea from a guy on Advrider.
13. ATF bottle holder. Automatic Transmission Fluid is a cheap and effective lubricant for chains. I apply ATF to my chain at every other fuel stop using a small bottle from The Container Store. I store the bottle in an old cellphone holder clipped to my pannier rack. I stole this idea from F650.com. For long trips, I strap an extra 1 quart bottle of ATF to the rear of my pannier using a Touratech bottle holder bracket.
14. Low profile turn indicators. The stock BMW front turn signals snap off the first time you lay your bike down. I bought cheap replacements designed for recreational vehicles and mounted them in place of the stock turn signals.
15. Fork boots. I chose neoprene fork boots from Cycle Gear to prevent my fork seals from failing prematurely. I have heard stories that the concertina style of boots restricts the air flow to the radiator in the F650 GS.
16. Voltage regulator relocation. The stock voltage regulator is located under the seat where it can't dissipate heat very well. A common modification is to relocate it to the exterior of the bike so that it doesn't overheat.
17. 12V outlet. I wired a 12V outlet from Radio Shack under the seat. I use it to inflate tires with a portable air compressor.