The one that got me hooked on the show was when Michael is going through the complaints Dwight has made and he claims Jim made him hit his head with the phone. My first thought was Dwight being paranoid but then Jim explains how he actually did it and I’m thinking, “Brilliant writing.”
But my favorite was when Jim convinced Dwight that he had faxed himself from the future that the coffee was poisoned. I want more of these memos from the future. 
I liked the one where Jim convinced Dwight he had the power of telekinesis by moving the coat rack back and forth. Although the real reason I liked it was the little smile on Pam’s face when she held up the umbrella she had used to rock the coat rack.
I’ve been working somewhat ‘back in time’ through the DVDs from when I discovered TO, (late in season 3 reruns, around ‘Product Recall’) and just recently got into season 2. Oh, my, the joys of the Jim/Pam friendship golden age, and the pranks that they conspire to play on Dwight.
Definitely love the ‘telekinetic Jim’ stunt at the beginning of Casino night, even if they couldn’t actually make it work as it was supposed to. (On the audio commentary, Jenna mentions that she couldn’t actually move the coat stand with the umbrella without being seen, and that they had a crew member tugging on it with a line too fine to be seen on camera.)
And Dwight’s talking head later, where he tries to stay skeptical and can’t resist the lure of planning what he would do if he had telekinetic powers.
ETA: Hey kunilou. Simulprank! 
Those would be precisely my two favorite also… if not for the discussion in the most recent episode about Battlestar Galactica. (I think it counts as a prank, given the context.)
There was an episode a couple of season ago (I think) where Dwight thought it was Friday but it was really Thursday. Jim and Pam reinforce his “it’s Friday” misconception by talking about what they are going to do tomorrow on Saturday and by discussing the Thursday night television shows that they supposedly watched last night. The next day, Friday, Dwight comes running into the office in the middle of the day, all disheveled. having just discovered what day it was.
I thought the text messaging that Jim and Pam did during the Man vs. Computer duel when Dunder-Mifflin infinity was rolled out at the beginning of season 4 was brilliant–and was made almost touching when Pam signed off by acknowledging “You are the Superior Being”.
The one when Jim came in dressed as Dwight and acting like him had me in stitches. “QUESTION: What kind of bear is best?”
The faxes from the future. Classic Jim/Dwight and a great way to carry on the torment while Jim was in another city.
Bit of a hijack this, but I thought all of them fail to measure up to the prank Jim played on Andy when he threw Andy’s cellphone (with self recorded ringtone) in the space above the ceiling. And then off course called him every 5 minutes.
Vampire Jim
And Dwight’s reaction to one of Jim’s Vampire moments while he was lining a box with glue. “One crisis at a time.”
I laughed out loud (something I rarely do) when I saw the stapler in jello.
Other than the ones already mentioned, I like when Jim hooked his Bluetooth headset to Dwights phone and forwarded his office phone.
“Gud afternoon mudder. I have married. Tell fahther.”
My favorite has to be the Pavlovian conditioning with Altoids.
ooohh totally forgot about the office articles (and wallet) in the vending machine, and then Jim gived him the bag of pennies to get his stuff out
Damn you…exactly the one I was going to mention. And I believe the bag had nickels.
One of my favorites is when Jim sends Dwight the “gaydar” metal detector wand and Dwight’s expression when he wands himself.
My favorite is the nickels in the phone, but I forgot how many good ones there have been.
–Cliffy
Well, I still need to get seasons 3 and 4… but my favorite so far is the “alliance” Jim forms with Dwight a la Survivor. Makes me giggle every time 
Unmentioned so far were the made up diseases for Dwight’s health care questionairre. They had one of tghe cast members on the radio and she said they were really trying not to laugh as Rainn read the names, and you can actually see it in some of the reaction shots