Most of Jones and Anderson's success were pre-USADA, some of Silva's opponents popped in his fight with them and I give Silva the benefit for the doubt because he was coming off a horrific injury in his 40's.
And people who write off Fedor because roiding in PRIDE was rampant are just being dumb.
A combination of the following criterias are what I feel make a fighter great: quality wins, titles/title defences or major tournaments won, impact on the sport, excitement, whether they brought that magic to the octagon, skill, overcoming the odds, well roundness, dominance, longevity, legacy, innovation, amount of fights, popularity, personal life and most important of all my opinion.
Obviously fighters today are more skilled than fighters of yesteryear so I'm judging skill in terms with the standard of their prime.
Honorable mentions:
Fabricio Werdum, Demetrious Johnson, Khabib Nurmagomedov, Takanori Gomi, Uriah Faber, Frank Edgar, Matt Hughes, Hayato Sakurai, Randy Couture, Ken Shamrock, Royce Gracie, Quinton Jackson, Wanderlei Silva, Masakatsu Funaki, Tito Ortiz, Chuck Liddel, Vitor Belfort, Dan Henderson, Michael Bisping, BJ Penn, Yoel Romero, Lyoto Machida, Mauricio Rua, Mirko Filipovic, Andre Arlovski, Robbie Lawler, Dominick Cruz, Gegard Mousasi, Jake Shields, Igor Vovchanchyn, Bas Rutten, Alistair Overeem.
My Top 10:
10. Conor McGreger - Low because he doesn't fight as much or have as many great wins as the rest but his impact on the sport is undeniable.
9. Shinya Aoki - His longevity and innovation is unmatched in the grappling department. Never fought in the UFC but fought plenty of tough fighters outside and while there were a couple of easy fights he would fight like 5 times a year. While he's not fighting the best right now he's still consistently fighting and winning to this day.
8. Antonio Rodrigo Nogueira - Most top 10 heavyweight wins. Had Fedor never existed he could have very easily took his place in this list.
7. Jose Aldo - Undefeated for 10 years. Mostly exciting, slowed down when he got to UFC but still exciting. Beat all the top guys of his era until McGregor.
6. GSP - Probably low to most. Never had an easy fight. Avenged all his losses(except Hendricks). Won belts in two weight classes. Loses points for boring fights and what is in my opinion some blatant ducking.
5. Kazushi Sakuraba - A guy who would probably be a lightweight by todays standards took on the best heavyweights and Light heavyweights in the world. His career has been spotty since the first Wanderlei fight and his prime didn't last as long as some but he undoubtedly brought a magic to the ring and his wins over the Gracies had a huge impact on the sport.
4. Daniel Cormier - Great career but like Nog to Fedor, he'll always be in Jones' shadow until he beats him.
3. Jon Jones - Has beat every other great light heavyweight of his era(Except Phil Davis). Would be higher but his loss to Matt Hamil holds him back.
2. Anderson Silva - Beating the most UFC wins record and smashing it as badly as he has paved the way for other fighters to do so. Brought new innovations to high level MMA striking as well.
1. Fedor Emelianenko - 10 years as the most dominant heavyweight, looked absolutely unstoppable for years, beat 99% of the top guys of his era, still looking good even today. It's foolish to write him off for never fighting in the UFC when Strikeforce had a tougher heavyweight division. Despite not being his old self, he's still a force. Incredible toughness as well. The GOAT.