I can only go by what I've actually seen as a real fan. I didn't start following and paying attention to the team until the early 2000s so here's my list for what it's worth:
1. Jason Witten - My favorite player of all time and probably the best all-around TE I've ever seen play.
2. DeMarcus Ware - The best defensive player I've gotten to see play for the Cowboys and the best pure pass rusher this team has probably ever had.
3. Tony Romo - Some might argue that he belongs at the top of this list, and I'd have a hard time disagreeing with them. Holds virtually every passing record in Cowboys history, and one of the most exciting players this team has ever had.
4. Tyron Smith - It might be a little premature, but this guy is looking like he's going to be one of the all-time greats at his position. He's still very young and has proven quite a bit in his short career thus far.
5. Terrell Owens - Going to be a controversial selection, but during the 3 years he was with Dallas, he was without a doubt the most explosive player this offense had and despite his antics, was one of the top WRs in the NFL during that time period.
6. Dez Bryant - Super talented, and scores a lot of TDs but he has a ways to go in the maturity department. He is one of the top red-zone targets in the game right now but needs to take it to the next level between the 20s.
7. Terrance Newman - He gets a lot of flack around here for some reason, but early on in his career he was the very definition of a shut-down CB.
8. Dexter Coakley - Despite his status as a running gag around here, he was probably one of the most athletic LBs I've ever seen play. Undersized, but was a all around great linebacker.
9. La'Roi Glover - A very talented DT who anchored our defensive line in the early 2000s
10. Roy Williams - He certainly fell hard from grace, but early on in his career I really thought that this guy was going to be what Ed Reed and Troy Polamalu ultimately became. He had coverage skills and was one of the hardest hitting players in the league. I really thought we had a special player for the first 4-5 years of his career.
Honorable Mention:
Sean Lee - would be up in the top 10 based on talent alone, unfortunately hasn't played enough games to warrant making the list.
Dat Nguyen - an underrated LB, and very solid throughout his career.
Miles Austin and Terry Glenn - Good receivers, just not good enough to make the top 10. Certainly two of the top 10 receivers this team has had since 2000, but not overall players.
DeMarco Murray - wasn't just a flash in the pan, IMO. He was a talented player before his record breaking year.
Larry Allen, Emmitt Smith and Darren Woodson - All time greats at their respective positions but their best years were behind them at this point in their careers.
Greg Ellis - Solid player, just never lived up to where he was selected in the draft (and who was ultimately passed over by selecting him)
Zack Martin and Travis Frederick - Looking like they're going to be great, but it's too early to tell.
Julius Jones and Marion Barber - Our RBs over the past decade haven't been anything to write home about, but these guys weren't scrubs. They could play, just never broke through to that next level.