ok, biggest thing is def exhaust. stocker makes wheelies easier, kinda like having a fat girlfriend on the back...
now once you touch the exhaust, you have to do air intake ('performance' filter/motobox), and fueling - PC/tuneboy, or dealer loaded AK map, so all this is really one mod, and #1 IMO
#2 for me, would be crash protectors. worth their weight in gold.
#3 - 1st/2nd gear retard elliminator mod - not a huge difference, but hey - it's free!
if you own pre-07, #3 would probably be sprockets
Suspension is VERY important, but I would argue that suspension setup is not really a mod... it's something you would adjust on every bike you get, and often change it depending on where you going (you would not use the same settings on bumpy back roads/highway/track) I see it kind of like brake/clutch/shifter leaver positions, or tyre pressure...