These are the Big Bang Theory episodes that I think rank up with the best of any sitcom. About two-thirds of them come from seasons 1 through 4. I don't think any of the best are from season 9 or the last half of season 8:

1:2 Big Bran Hypothesis: Sheldon and Leonard clean Penny's apartment
1:4 Luminous Fish Effect: Sheldon gets fired from his job
1:10 Loobenfeld Decay: Sheldon and Leonard try to avoid attending Penny's musical showcase
1:16 Peanut Reaction: Sheldon's surprise birthday party
1:17 Tangerine Factor: Penny and Leonard both stress out before their first date

2:3 Barbarian Sublimation: Penny plays Age of Conan
2:5 Euclid Alternative: Sheldon learns to drive
2:7 Panty Pinata Polarization: war between Sheldon and Penny
2:11 Bath Item Gift Hypothesis: Sheldon shops for Christmas
2:13 Friendship Algorithm: Sheldon learns how to make friends
2:18 Work Song Nanocluster: Sheldon and Penny make Penny Blossoms
2:22 Classified Materials Turbulence: Howard discovers that his space toilet doesn't work

3:5 Creepy Candy Coating Corollary: Sheldon catches up with Wil Wheaton
3:14 Einstein Approximation: Sheldon is stuck on a physics problem
3:16 Excelsior Acquisition: Sheldon goes to court
3:18 Pants Alternative: Sheldon receives an award and makes a speech
3:22 Staircase Implementation: how Sheldon and Leonard met
3:23 Lunar Excitation: Raj and Howard submit a computer dating profile for Sheldon

4:1 Robotic Manipulation: Sheldon and Amy's first date
4:2 Cruciferous Vegetable Amplication: Sheldon tries to love forever
4:3 Zazzy Substitution: Sheldon and Amy break up
4:4 Hot Troll Deviation: Howard tries to get Bernadette to take him back; Sheldon and Raj share an office
4:5 Desperation Emanation: Amy wants Sheldon to meet her mother
4:9 Boyfriend Complexity: Leonard meets Penny's father
4:13 Love Car Displacement: everyone is on a panel at an academic conference
4:20 Herb Garden Germination: Sheldon and Amy spread a rumor
4:21 Agreement Dissection: Priya invalidates the Roommate Agreement
4:23 Engagement Reaction: Mrs. Wolowitz meets Bernadette

5:2 Infestation Hypothesis: Penny finds a good chair on the curb
5:10 Flaming Spittoon Acquisition: Amy becomes Sheldon's girlfriend
5:17 Rothman Disintegration: Sheldon and Kripke compete for an office; Amy buys Penny a portrait of them both

6:4 Re-Entry Minimization: Sheldon and Leonard compete in a series of contests against Penny and Amy
6:9 Parking Spot Escalation: Sheldon and Hioward feud over a parking spot
6:21 Closure Alternative: Sheldon cannot leave things unfinished

7:3 Scavenger Vortex: a scavenger hunt
7:14 Convention Conundrum: Sheldon starts his own version of Comic-Con

8:7 Misinterpretation Agitation: one of Penny's customers falls for her

Edit: 9 years later, and having considered the episodes from Seasons 10 through 12, I still think "The Misinterpretation Agitation" (the Billy Bob Thornton episode) remains the last must-see episode. There's a lot of good material after that, but no episodes that are clever throughout.