When selecting Psionics as a skill, the description reads "No! Not the mind probe!", referencing Doctor Who.
One of the Psionic abilities lets you Nerve Staple enemies like in Alpha Centauri.
Fellow indie game Dwarf Fortress gets tons of them. The biggest might be the ever-present ludicrously bizarre names randomly generated for all places and artifacts, one of Dwarf Fortress' famous traits.
The description for the highest difficulty setting is the official DF motto "Losing is Fun!"
The description for the "Shoddy Dwarven IED" trap reads "This is a sub-par Dwarven IED design. All craftsdwarfship is pretty lousy, actually."
The Plump Helmet is named for the food crop mushroom grown by dwarves in Dwarf Fortress, and its description reads "This helmet was crafted by dwarven smiths in ages long past from the weapons cast down by the dying goblins foolish enough to attack their undermountain fortress," a nod to the common strategy of salvaging metal from weapons dropped in goblin assaults.
The steel ingot description read "The steel ingot is a testament to the fact that you'd really rather be playing some other video game with a more finely honed crafting system. Oh well...". It is created by mixing chalk, coal and iron, which is similar to the way it is created in Dwarf Fortress (and indeed, in the real world).
The tooltip for Conflagratory resistance mentions "Strange Moods" which are a random thing that can happen in Dwarf Fortress
The Secret of Monkey Island gets at least two: the flavour text for Grog uses part of the game's recipe, and The Helm of Guybrush.
A Golden Axe is present as a unique weapon, complete with Lampshade Hanging on how impractical gold is for a weapon metal.
The Aluminum Tube's description: "This is irrefutable evidence of Dredmor's nefarious plans." Compare to this Star Control II quote:
Fwiffo: As yet, The Ultimate Evil remains largely unmanifest, and its powers and exact intentions are still a bit obscure ... since it lurks just outside the range of even the most sensitive, long-range detectors ... which we feel gives conclusive evidence as to The Ultimate Evil's nefarious intent.
The "My Little Anvil Junior Smithing Kit]]" speaks for itself. Smithing IS magic! (On the minor chance you don't know the reference, it's a My Little Pony Friendship Is Magic.)
The level-up screen says things like "Your princess is in another castle" (misquoting Super Mario Bros), "It is dangerous to go alone! Take this" (The Legend Of Zelda), "Power Level 1,370" (Dragon Ball Z), "Conan the Librarian" (a Film/UHF reference, itself a parody of Conan the Barbarian), and "The Blue Thunder of Furinkan High" (Kuno's self proclaimed moniker in RanmaOneHalf) just to name a few.
One of the higher-tier pieces of headgear you can find is a red, wide-brimmed Vampire Hunter's Hat (identical to the hat worn by the protagonist of Hellsing), which according to the tooltip "isn't really suited for vampire hunting, but what can you expect out of someone who thinks that spelling 'DRACULA' backwards is a good way to hide their identity?"
The original title screen, the head at the bottom of the screen, and the graphic design of Floor 3 are all shout outs to Doom. One of the armours originates from Doom, while equipping a helmet based off Quake along with it, gives you a "Realms of the id" achievement. One of the audio tracks is also a Suspiciously Similar Song version of the Level 1 tune from Doom 2. Continuing the theme is the Interdimensional Axe - it's the Quake axe!
The bolstered list of Steam Achivements released July 19 are pretty much ALL shout-outs. See the wiki for details.
And in the fungi, there's the Plumber's Agaric (providing a strength buff), and Niccolo Machiavelli's The Prince ("A regal mushroom better feared than loved.").
If you happen to encounter a Game-Breaking Bug that makes the game crash (Most infamously the, fortunately fixed, save-game incompatibility of the latest patches), you get an achievement called "Suddenly the dungeon collapses!", which was a possible event in Nethack.
"Lutefisk For The Lutefisk God" — not to be confused with the Warhammer god Khorne's "Blood for the Blood God." (Although the two are old poker buddies.)
In the tech-based floor, the chests look suspiciously like a certain Portal puzzler's famousbox.
The Rage skill tree is full of pledges in the general direction of "For Crom!" (Conan).
Equip a full set of clockwork limbs and weaponry to get the "I Didn't Ask For This" (Deus Ex Human Revolution) achievement.
The Assassin description mentions that there's something about a creed.
The fire arrows are best used against thatch-roof cottages (Homestar Runner).
"Haywire Chance affects how likely your spells are to trigger a highly unstable resonance cascade event" (HalfLife)
A low-level footwear item is named "The Flippy Floppies", a possible reference to The Lonely Island's "I'm On A Boat".
With the expansion coming soon, there are a few more achievements and items with even more shoutouts! One in particular is the Parachute Pants, which give you an amazing +10 Dodge skill, which means the monsters literally Can't Touch This! (MC Hammer)
Equip the Warhammer as well for the achievement "You Know What Time It Is".
The Root of T'char from Zalgo can be found and eaten. Doing so will kill you if you're not prepared.
One of the creatures' messages appears as "Killing me won't bring back your honey." (The Wicker Man)
And the achievement for dying from thaumites is "Not the Bees!"
One demi-artifact armor piece is a Mad Max-esque black leather jacket with one-sleeve. It can be combined to make the Magical Badass Jacket, whose description is "Do you feel magic? Well do ya, punk?", referencing a similar line in Dirty Harry.
The descriptors for "New Bolt" and "Bolt Classic" should be more than a little reminiscent of one of Coca-Cola's gaffes.
The Archaeology skill tree is loaded with Indiana Jones references, including a skill called "It Belongs In A Museum". You even start out equipped with a sufficiently Nice Hat.
Two abilities in the Viking Wizardry tree reference the Rhapsody of Fire songs Triumph For My Magic Steel and Unholy Warcry.
The message log has a few random lines, including "You can't cut back on funding! You will regret this!" (SimCity)
Mace of Windu (named after the character in Star Wars), which is practically a lightsaber in apperance and (most of) stat, although is considered to be a mace.
