Here are some of the more common farkles:
Centerstand- Makes maintenance much easier
Madstad Bracket- Allows a large adjustability of the stock or aftermarket windscreen. Many also get a different screen or mirrors to reduce buffetting.
Fork Brace- Improves handling dramatically
Crash Bars- Dropping it once pays for the cost of the bars
Replacement seat- The stock 1000 seat can be found cheaply and is more comfy (higher and wider). Suzuki makes a reasonably priced Gell seat that is very nice for the money. Also, there are many aftermarket solutions from sargent, corbin, mayer, russel, etc. IMO the v-strom seat isn't bad for a stock seat but if you want to do some serious traveling you will want to upgrade.
2006 Wee: Farkling in progress