These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Tropes for the tabletop game
Complete Monster: Toxic mages and insect shamans. Toxic mages view others as obstacles to destroy and the world as undeserving of continued existence. Becoming an insect shaman means willingly allying with Eldritch Abominations from beyond the pale who invade reality through living hosts. If an insect shaman is found in the area, its remaining lifespan is measured in initiative passes.
Darkness-Induced Audience Apathy: See main entry for details. Brief recap: the 3e and early 4e sig characters were largely antiheroes. The current 4e sig characters are rapists, vivisectionists, spree killers (who in 3e were specifically held up as examples of bad shadowrunning), and amoral assassins. Oh, and FastJack, grand old dean of shadowrunning, is now starting to go senile, though this turned out to be a red herring...
Game Breaker/Elite Tweak: Third Edition has an Edge called "Connected" that, when taken for a vendor contact, allows you to buy from that contact at the list price or sell at the street price, which can be as much as three times more. Thus, taking that edge for two contacts (one to buy from, one to sell to) allows a player to get ridiculous amounts of money while the GM isn't paying attention.
A troll adept, with only three points of Magic and the right skills in 4th Edition rulebooks, could pick up a paperclip and explodes someone's head by throwing it really hard.
The physical adept can become noticeably broken if you use initiation to offset the Essence cost of cyberware.
The chemical DMSO. If you splash it on someone, it allows for other chemicals to be absorbed into the DMSO-coated skin. Additionally, armor has little to no effect, so if someone hits you you with it, you WILL be affected. The end result being that if you mix DMSO with poisonous drugs and load it into a squirt gun, you get a super soaker that deals one-hit kills. You can hear details about how this can affect a game environment in this video.
Tar Pit ice in matrix runs, a hidden secondary ice which will erase whichever program you're using if it fails and up the alarm rating to Red. Since Deception and Attack are basically the only two ice you'll ever use, this has a 50/50 chance of forcing you to abort a run entirely. It doesn't matter if you have a fully-upgraded deck, either; chances are good you'll trigger it. Keeping weak programs as a sacrifice is pretty much the only reliable way to keep on moving through the high end systems.
Hell Hounds in the real world. They travel in packs, move extremely fast, and hit like a ton of bricks. Until you get high end armor and weapons, an encounter with them spells death for you.
Game Breaker: There's a shop that will buy stolen data. This is easily the most profitable activity in the entire game, enabling you to quickly upgrade your deck to steal larger and more valuable files, in addition to making it trivially easy to obtain all the best equipment. To give an example of just how broken it is, a single-run on a high-end system will near-certainly net you three times more cash than a shadowrun from even the most well-paying client, and that's at a minimum. A single file from the big corporations can be worth three times as much as a single shadowrun, sometimes even more. You can even do it in tandem with a hacking shadowrun to get the karma payout in addition to the money.