While I didn't exactly run, my favorite "I'm pretty sure I'm boned" moment came from Alien vs Predator (1999 version). For those who are unaware, this game had some serious balance issues with regards to the predator. It had vision modes for every kind of creature in the game, with certain weapons this gave out auto-aim and literally EVERY weapon could kill a marine in one shot. By contrast, it took the better part of a 100 round magazine to the head from a pulse rifle to drop the predator. Worse still, while the marine had to hunt for weapons, ammunition and armor, the predator had all his weapons from the start and carried around a self heal kit that gave full health in exchange for half your total energy store (which took perhaps a half minute to a minute to reacquire. The worst offender of all however was the disc - while it moved slowly enough to be doged if you had some range, in a large enough room it simply killed you on the second pass, and if not that you generally got shot with plasma, or killed by a spear gun or punched to death while desperatly trying to avoid the whirling instant death machine. Suffice it to say, even an utterly unskilled predator player was more than a match for a handful of skilled marines.
Sadly, no one else actually wanted to PLAY as the marines.
My stoy comes from a game of last man standing, where I an a small team of marines were tasked with simply killing the predator. Since this was unlikely, victory was also awarded to the last marine left alive. In spite of our best efforts, within minutes our numbers dwindled and in short order I was left to my own devices. As luck would have it however, I was not completely screwed - I had acquired both the grenade launcher AND the smart gun. Knowing simply hunting around in the dark for the predator would end the same way it did for everyone else, I hatched plan. This level had a particular room with only one entrance or exit for any character (even the aliens had to use the door like a civilized species)(technically it was outside the ship but it was more literally just a largish (for the game) room. After placing six(6!) proximity grenades around the door, I found the best cover I could find that gave a straight run at the door and leveled the smart gun at the door, occasionally pausing to refresh my flare pile so I could see without resorting to putting away the motion tracker. For an eternity I waited (much to the delight of the other players I'm sure).
Eventually, my quarry wandered into my cunning trap, and I heroically sprayed smargun rounds into the fireball while I bolted for the door (This game had deformable explosions - thus my plan actually resulted in a fairly severe injury to myself). Unfortunately, I had hoped against all logic that my trap would have already laid him low but alas, it wasn't sufficient. Without a better plan than "Try the same thing again on the other side of the door" I placed my last six proximity grenades on the door. I waited for the predator to peek around the corner (not quite enough to trigger the blast) and sprayed off a burst from my pulse rifle hoping to draw him in for the kill. Again my cunning plan paid off and he walked through a second stack of grenades. As the hellish noise and flames died down, I noted rather glumly that I had not been given a kill notification but I absolutely KNEW the guy had to be low on health since I had used enough firepower to bring down the Sulaco on the thing.
With nothing left but a pulse rifle I turned the corner and saw the predator backing away to a corner, and knowing that this was the only chance I'd have at it I opened up. Dozens of rounds found their mark to no avail and I noted (to my utter dismay) that he had begun the healing process. Desperate, I fired off every pulse rifle grenade I had in my arsenal and through a streak of fantastic luck managed to snag him in the head. It was one of only TWO times I ever killed a predator by myself in that game, and by far the more epic of the two bouts.