1. Fedor = champion in multiple organizations, in multiple sports; reigned over the heavyweight division when Pride was the top organization; undefeated for a decade, with no losses during his prime; defeated several all-time greats; great longevity in the sport
2. Henderson (Dan) = two division champion in a top organization; defeated multiple all-time greats, at multiple weight classes; great longevity in the sport; can protect his ranking by finishing off his career with a couple of solid wins
3. Anderson = reigned over a tough division for multiple years; defeated multiple all-time greats; champion in multiple organizations; great longevity in the sport; can save his ranking by finishing off his career with some solid wins
4. GSP = reigned over a tough division for multiple years; avenged all of his losses; defeated several all-time greats; retired during his prime, so will most likely drop in the coming years
5. Jones = reigned over the marquee division during his era (current); undefeated, with victories over several all-time greats; young career, no indication of longevity; Jones is the likeliest fighter to move up over the next couple of years
6. Shogun = the only fighter to become a marquee champion in both of the premier MMA organizations; several victories over all-time greats; multiple injuries, harming his longevity as a top fighter; is no longer able to fight to his potential
Rounding out the next couple of spots would be: Wanderlei, Vitor, Liddell, and Penn. I don't have an order for these four, but you have to give a lot of credit for their belts and respective reigns (Wanderlei, Liddell, Penn) and their longevity (Wanderlei, Vitor).
When you're talking about the "Greatest of All-Time" list, I think you have to consider championships and longevity, more than you have to consider short-term heights of talent. There are some fighters who were untouchable and extremely talented for a brief period of time, but could not last at a high level. These I could not rank up as high as someone who reigned over a tough division for multiple years.