In order to make this list, said TF2 mechanic needs to (1) heavily affect some aspect of playing the game normally, (2) be completely unexplained or hidden, and (3) be something I somehow only learned in 2016 despite my pathological addiction to analyzing every facet of this game. I’ve divided the list into three “major” and three “minor” mechanics.
Major 1: Projectile Models on some weapons affect aerodynamics. Several of the projectiles in TF2 actually care about the drag on the fired projectile, which means that, for example, most of the grenade launchers fire even more differently than their stats would suggest. Here’s a thread with videos where sigsegv, the person who discovered this, leaves very detailed notes on the phenomena. The most egregious example are the two bread reskins for Mad Milk and Jarate, as the larger models make it possible to throw them further than their free-to-play equivalents.
(Sigsegv has a Youtube channel full of obscure TF2 mechanics just like this, if this sort of thing interests you I highly recommend checking it out!)
Minor 1: Degreaser cannot deal mini-crits. Due to the way weapons deal damage in TF2, every tick of flame from the degreaser rounds down (i.e. completely removes) the damage boost from mini-critting. If a burning soldier is running for a health pack, he might as well pull out his Escape Plan and get there faster.
Major 2: You can’t chat while dead. Have you ever posted something in chat after getting killed? “Nice airshot!” “Dat random crit…” “Hey, that’s what I named my pan too!” Well, the enemies weren’t seeing it. There’s a complicated set of criteria to prevent living enemy players from seeing what dead/spectating players are saying, and I can’t believe I never knew this. How many of my messages have gone completely unread? I almost feel Valve needs to make this clearer, or preferably just remove it.
Minor 2: Kunai can make sentries forget about you. Normally, when a spy disguises in sight of a sentry, the sentry remembers that you were a spy and keeps shooting. But if a kunai spy disguises in view of a sentry, the sentry blithely forgets about him and treats him like a teammate. This unintentional side effect came about because the kunai was originally created from the Your Eternal Reward, which also has that effect because otherwise backstabbing engineers would be almost impossible.
Major 3: Crouch Jump Exploit. This one is extremely simple to pull off and can badly affect a sniper’s ability to headshot you. This thread contains links to videos that go way more analytical than I’m prepared to, but in a nutshell just mash the crouch button while in air to send your hitboxes all over the place. Jumping like a spaz is already a time-honored attempt to avoid getting headshot so adding some crouches can’t hurt. And speaking of snipers…
Minor 3: Sniper rifles can detect invisible spies. The laser point will recognize when an invisible spy is in the crosshair and size itself accordingly. Only useful if an invisible spy is significantly closer than whatever map ambiance is behind him, and requires eagle eyes on the sniper’s part, but on the other hand you should be that observant if you’re choosing to play Sniper.
Major 4: Holding left-Alt lets you move your character with your mouse. Harken back to the days of DOOM! This can be really useful for precision placements or hugging cliffs, and works in most Source games. If it doesn’t work, you’ve probably unbound it at some point, and binding any key to “+strafe” can make it possible again.
If you’d like to read more, there’s some good stuff in this thread that I only found while trying to find a featured image for this article.