Since it's my favorite universe to play in at the moment, let's start with Stargate Atlantis:
I really like Ma'hal's vids. My favs are: Cream in my Coffee (snerk), Crazy Faith, If I Were Gay (double snerk), From A Shell, It's in His Kiss, Rock Steady, and the ever-popular Love Shack, in no particular order of preference. Crazy Faith and From a Shell are very touching and emotionally well-done. The others are just plain fun.
Another vidder who's made some amusing vids is K.M. Anderson/Coffee Cat Productions. I'm sorry, I can't find the url/website where she has these available. If anybody out there knows the url/availability of these, please write. The one I really like is "Johnny FeelGood", song by Liz Phair. (Contact me if you would like to see this one.)
I really, really like this vid by Nel at http://www.pertifity.com : "Once More (With Feeling)", an excellently crafted instrumental piece vid. Her "Apocalypse, Please" also packs a punch.
Of course, any vid done by wickedwords is a plain KO in one punch. I adore "Hallellujah", and "Stress" is five star, stellar all the way. Get it here:
That's all I can think of off the top of my head...and now I've got these listed where I won't forget them, either. Chime in with more recs if you've got them.