A giant stone ring that takes the player back in time to before Vault 13's water chip broke. The stone ring itself is a reference to the Star Trek episode "City On The Edge Of Forever.''
A group of men in power armor claiming to be King Arthur and his knights, who ask if you've seen the Holy Hand Grenade Of Antioch. A Dummied Out (and restored in the Restoration Project mod) second encounter features them fighting (and most likely getting slaughtered by) a vorpal rat, with the Holy Hand Grenade as droppable loot.
Related to the above, the player can also find themselves having to cross the Bridge of Death, but first they have to answer the bridgekeeper's three questions: "What is your name?" "What is your quest?" and then a random question pertaining to fairly obscure Fallout trivia. Failure is punishable by instant death, but it's also possible to answer the third question with a question, whereupon the bridgekeeper explodes messily.
The "Tin Man" (really just a man in Enclave power armor that has rusted into immobility and needs to be oiled.)
"The Unwashed Villagers hunting a spammer" (referencing an occurrence on the Interplay forum, where a Troll called The Grim Reaper continuously harassed a Fallout fan community called the Unwashed Villagers.)
Asking Dex, the third of the Dummied Out recruitable NPCs what life was like before the end of the war will have him spin an outlandish tale featuring, among other things, Godzilla, Ferris Bueller and the Tarrasque.
Another one to Monty Python. In the Den, a dialogue with Mom the diner owner is a shout-out to the spam sketch:
Mom: We just have rat-pie, rat-loaf, and spaghetti. Chosen One: Uh, could I get something without so much rat in it? Mom: You could have the spaghetti. It doesn't have too much rat in it—just the sauce, that's all.
A reference to the Church Police sketch, in Redding if you ask the Sheriff how he knew you were a ranger he tells you that it's tattooed on the back of your neck.
The description text of the Magnum .44 revolver includes the famous quote of Harry Callahan about feeling lucky.
The game Tragic: The Garnering, which the ghoul Wooz in the town of Gecko plays, is a parody of Magic: The Gathering.
A crashed plane with the remains of Amelia Earhart hanging out of the cockpit.
A liquid metal brahmin named the B1000 that spouts Terminator quotes.
A bazaar where the party can purchase the Devilthorn Jacket, a reference to the Demonspike Coat from Diablo (and completely unwearable due to having the exact same stat requirements.) The people in the bazaar also spout common MMORPG player lines (in particular from EverQuest.)