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Metroid Prime 3 :^)
Totally Radical Awesome Game
The beginning of Jade Cocoon features 10 minutes of unskippable text mashing. Only way to go faster is to mash faster.

Chapter 5 of Soul of the Samurai pits you against an endless horde of zombies. However attacking them slows the game down, so it's faster to hide in a corner and do nothing for about 5 1/2 minutes.
Edit history:
Zergreenone: 2015-10-03 06:41:06 pm
Zergreenone: 2015-10-03 06:40:56 pm
Zergreenone: 2015-10-03 06:40:11 pm
Zergreenone: 2015-10-03 06:36:50 pm
20 minutes of boredom (starcraft terran 03):

Quite possibly the longest wait time in an optimal speedrun of a game that has a run that has been accepted to sda
I've read all the replies again but I've dropped the idea of classifying everything, so here's some individual comments whenever I was left with anything to say:
GTA3/VC: Patrick - Do it at ESA where literately ahtninyg geos.
Braid: I see. That's what I'd call a forced wait. (cloud star)
Starcraft 1: Ah, yes. I know lots of RTS games have similar autoscrollery missions. I'm reminded of Age of Mythology where the last mission has a 30-minute timer but that's not technically all wait time because you're building units most of that time. StarCraft II has a mission that you can turn into a long wait time (The Dig). I just started another thread for stuff like that...
Metroid Prime 3: You're expecting people to get what you mean?
Jade Cocoon: Definitely doesn't count because inputs make it faster.
Soul of the Samurai: That sounds better. If you don't have to defend yourself in any way or reposition then it certainly counts and is quite interesting too because it's not forced behaviour. If you've got a video to link go for it (use the hidden tag).
Starcraft 1 (again): Okay that certainly looks like a thing. Is there no inputs at all during the wait time?
Glitch advocate
Longest wait in a game I've speedran is in God of War: Ascension. God of War-games are typically pretty cinematic, but Ascension is easily the most cutscene-heavy of the series. The longest single wait in the run is near the end, where there (on NG+) is a 3 minutes 20 seconds long string of cutscenes where you don't have any control.

I guess any really cinematic game (L.A. Noire, Heavy Rain, etc.) is a good contender for long wait times. I think in Beyond: Two Souls there are stretches of over five minutes where nothing can be done to speed them up.
No essential inputs for about 18 minutes. I believe I selected an SCV at one point to make him pick his nose since I wasn't taking it seriously enough.
Edit history:
LotBlind: 2015-10-03 12:32:59 pm
Zergreenone: Okay, that seems to take the lead then! Cheesy I'll call that longest timer wait, with other categories being longest unskippable cutscene, longest forced wait and longest safe autoscroller. Difference between "timer" and "forced wait" is a forced wait restricts your movement so everyone who plays the game needs to stand still to get past that part (like Earthbound), while a "timer wait" allows you to do all or most of your usual things and different players may spend the time differently, as in your case or in Quest for Glory 2.

Longest unskippable cutscene speaks for itself, but may involve several consecutive cutscenes with no inputs in-between (not even to confirm a savegame or anything at all). Longest safe autoscroller is, of course an autoscroller that you can survive without giving inputs as in the Sonic and Tails flying stage, timed from the moment when you've reached the safe spot.

I'm sure that's far from adequate but I'll see if I could fit everyone's examples into a neat paradigm after all. Remember I'm still only looking for runs that have passed verification or are otherwise of high quality.
In Secret of Evermore when you go to the market you have to wait 15 minutes for it to close and the next part of the story to occur.

http://speeddemosarchive.com/SecretOfEvermore.html
In Beyond Two Souls, The Dinner has you wait around 10 minutes for your date to show up. And, that's with the pizza speedup.
Those two sound like timer waits. So Starcraft keeps the lead there.

Doesn't anyone have a longer safe autoscroller than Sonic and Tails?
Enigma has a minute-long forced wait in one of its levels. (Strangely enough, for many years the IL time for that level was less than a minute, because pausing the game froze the in-game timer but not the forced-wait timer. That's changed since, though, and the old records were invalidated.)
Edit history:
mrprmiller: 2015-11-20 05:49:20 am
Everyday is puppies and sunshine...
LotBlind, I figure I'd mention it here, but I'm chopping away at some of the QFG2 wait times in Raseir.  Not sure how I triggered it yet, but I got the first wait chopped by over a full minutes.  :/  (Expect an updated run.)  Since QFG5 has been thoroughly decimated, I'm throwing some time back at QFG2 to make this section as fast as possible.
Sorry pr, no idea how I missed your post here. Looking forwards to a new submission of QFG2 then! But you shouldn't have said anything, now you're certainly out of the running for this challenge! :/
Everyday is puppies and sunshine...
Well, I'm not sure.  I haven't been able to duplicate it.  :/  I threw a glitch together somehow and happened to get a good recording of it during a serious attempt (sub 17 minutes now). 
That's pretty lucky! Ha! Tongue