Flair had so many really good world title matches it's hard to pick just one. The match mentioned in this thread against Jimmy Garvin was an excellent match (steel cage) from the 1987 Great American Bash.
His best opponents were probably Dusty Rhodes and Sting. I would say Flair's best match with Rhodes was probably Dusty's title win in the cage at the 1986 Great American Bash. The Title Unification Match with Sting mentioned earlier in this thread was good (from 1994, this match lead to Hulk Hogan's arrival in WCW) but I think their best match was the 1988 Clash Of Champions. That match more than any other put Sting on the map and got the wrestling public to notice him as a legitimate main event star.
Certainly the Flair/Steamboat matches were always good, with their 1989 series being considered by most experts as one of the best main event programs in wrestling in the last thirty years. PPl still rave about those matches. It's hard to pick which was best, although I would vote for the middle match, the best of three falls bout where Steamboat was champ in the Super Dome in New Orleans, a 54 minute marathon.
Flair also had phenomenal matches in 1987 with Barry Whyndam. Their hour long match on NWA WorldWide Wrestling program is probably the crown jewel of the first Flair DVD WWE did in 2003. Their final match in the series, at the Crockett Cup Tournmament, was also 5 star quality. Whyndam never looked better than he did in those matches that year.
Speaking of never looking better, check out the WWE's Starrcade retrospective DVD and watch the Flair/Lex Luger match from Starrcade 88. A fast paced, non stop, 33 minute battle in which Luger looks 10 times better than he ever did against any other opponent. Proof that Flair in his prime could make average wrestler's look really good and really good wrestler's look great.
Flair's wrestlemania match against Randy Savage also deserves consideration. The entire match against the backdrop of the feud that preceeded it was pulled off almost perfectly. If you were picking Savage's best matches this would be in your Top 3.
Flair's performance in the 1992 Royal Rumble has long been considered one of the greatest in Rumble history. The number of main event stars in that match (Hogan, Savage, Jake Roberts, Undertaker, Sid Justice, Shawn Michaels, Roddy Piper, Ted DiBiase) plus former world champions like Sgt Slaughter and Kerry Von Erich, this was a rumble line up to die for. Flair took every big press slam, over the top rope clothesline, turnbuckle flip, etc you can think of and bounced around non stop for 62 minutes, selling virtually everyone's best moves. Flair's expression at the 30 minute mark when he collapses in center ring after eliminating Von Erich and Boss Man, only to see Piper making his way to the ring, is one of the classic Flair moments in his career.
Flair's 1994 Great American Bash match against Hulk Hogan deserves honorable mention, especially since this is probably one of the two or three best matches Hogan ever had.
The 2006 TLC Match against Edge for the WWE Title also deserves mention. Flair was 56 years old and took multiple falls off the top the ladder, bled everywhere, and he and Edge worked the crowd like crazy, keeping everyone on the edge of their seat till the final bell. This match was probably the best match Flair had in his last hurrah with WWE, slightly ahead of his 2003 World Title Match with HHH or their 2005 Hell In A Cell Match.