Since the subject popped up on this blog last week. (Missables caused by glitches don't count, in the interest of fairness, so that leaves out the Deku Nut upgrade from some releases of OoT, for example.)
My vote goes to the Ing Webtrap scan from Metroid Prime 2. Would you believe some people use the "the camera zooms in on it, so you should know to scan it" excuse? Bullshit. In every single Metroid Prime game, any instance of you being locked in a room to fight enemies is done by a standard locked door... EXCEPT this one. Now the big problem is that while such missable scans are fairly common in those games, this one happens in the heat of the action. You have to remember to take a few seconds of your time to just take those hits from the Ing that are relentlessly attacking you just to scan the thing. Most other missables, like the Lightbringers and Weblings in the same Dark Agon area, are located in places where you're in full-on exploration mode, so you're less likely to forget to scan them. The Ing Webtrap, on the other hand? Nope, you're too busy fighting. Fuck this thing.