sorry, anything that has brendan fraiser in it can't really be that good
I thought that too, and while I like this show I don't watch it much. I caught this episode without even knowing Brendan's character (apparently he was in another episode.) It's really touching and well written, and if you don't look for the twist it can blindside you. Now, it might have been the beer, but I busted out crying at the end of the episode. It was really powerful and I'll never forget it.
Best thing Brendan Fraser has ever touched, like you I didn't think he had it in him.
In fact, I almost didn't read this topic because I figured a Scrubs fan would have a different favorite episode and I didn't feel like arguing with him when I likely hadn't seen his episode. I don't see how there could be a better Scrubs episode, it's up there with the most memorable sitcom episode of all-time for me.