None really spring to mind, when you think of really amazing Smackdown! matches. I mean, when thinking of RAW you think HBK/Cena, HBK/Benjamin, Austin/HHH vs Benoit/Jericho, Christian/RVD, etc. What springs to mind for you?
Eddie Guerrero vs. Edge in a no DQ match from 2002 is way up there for me.
I remember Lesnar/Angle in an Iron Man Match being quite good. It had some of the problems Iron Man Matches have but it was still a damned fine match.
Chris Benoit vs. Steve Austin in late May 2001 is one of the best singles matches in the history of Smackdown, I'd offer.
Also, spring and summer 2009 has a lot of fine, fine work from individuals such as Chris Jericho, Rey Mysterio, CM Punk, Edge (before the Achilles tear) and John Morrison. I remember Morrison/Edge being given something like 20 minutes on Smackdown and I have to say, it rocked. So did the series Punk and Morrison had with each other that summer. And Jericho/Mysterio had some good encounters, especially a rematch from The Bash (the match at The Bash being MOTY).
Orton vs. Christian from last year was a tremendous match, too. (The match that started the entire feud right after Extreme Rules.)