Mêlée à Trois: In one mission, you have a red dragon and a tribe of fire giants that you need to get rid of. How it usually works is that you make a deal with one to help you fight the other. Being Chaotic Evil, whichever one you ally with will betray you after the other is defeated. You can, however, choose to fight them both at once, resulting in this trope.
Modular Epilogue: At the end of the game, the player is shown what happens to various locations and people who were influenced by the PC's decisions. For the ending itself, though, there are only two options.
New Game+: Officially exporting characters lets you take them to a new module on the rare chance you find ones with end level and start levels that match up; unofficially it allows you to repeat the campaign at level 20.
Never Found the Body: Zhjaeve is the only party member that isn't confirmed to have lived or died during the collapse of the Vale.
Non-Lethal K.O.: Only in the first game and Mask of the Betrayer. Storm of Zehir plays it closer to the pen-and-paper rules: if a character reaches -10 HP, they're dead and have to be resurrected with a spell.
Non Standard Skill Learning: In Mask of the Betrayer, increasing your Relationship Values with party members unlocked bonus feats (mainly skill and ability boosts applied to both you and the party member). Meanwhile the Storm of Zehir expansion has a list of Teamwork Feats which require two steps to unlock: meet requirements outlined in the game manual, then accept and complete a corresponding sidequest from the Adventurers' Guild at Crossroad Keep. All three games also give history feats for completing story requirements, and in SoZ some of them grant bonuses.
Obvious Beta: Obsidian has a well-deserved reputation for this. Despite not looking much better visually than KOTOR, NWN2 is somewhat of a hardware hog, and it suffered from memory leak issues and a lack of polish. Then both expansions managed to break the previous campaign on release.
Oh My Gods!: Used heavily. To name just a couple of examples, during the Battle of West Harbor one of the militiamen blurts out "Cyric's blood!" and Khelgar's "swear" emote is "By Tyr's right buttock!"
Mask of the Betrayer has a golem you can reactivate in the starting dungeon. It craps out when you escape. Much later, if on the Fugue Plane you choose to defend against the Crusade instead of leading it, Kaelyn leaves the party and Kelemvor gives you Araman to replace her.
Those two are also guilty of it due to poor game mechanics, as they refuse to teach anyone how to use the Kryptonite Factor during the final battles, even if the storyline makes it clear the PC should be just as capable as either of them.
Randomly Generated Loot: While not standard, this is possible when creating a module through using its scripting language. It is actually done in the "Diablo - The Dark Wanderer" multiplayer module (running on the Viking Northeast server) to imitate the way the Diablo game generates its loot.
The OC uses the system from Neverwinter Nights and Baldur's Gate: resting takes six seconds, fully heals you and replenishes your spells, and only requires you to be far enough away from any enemies. The only thing it can't do is remove diseases (not every time, anyway) and curses.
Mask of the Betrayer quite thoroughly upends the system. Resting now causes eight hours to pass on the In-Universe Game Clock, which, after Mulsantir, raises your level of spirit hunger and brings you closer to a Nonstandard Game Over.
Storm of Zehir also causes eight hours to pass, you can't rest in dungeons at all, and if you make camp in the wilds you may be at risk of getting caught flat-footed for a Random Encounter (in other words, the enemy gets a surprise round). There are items and teamwork feats to reduce the risk of the latter.
Also potentially the Knight Captain. This troper had him as a bard/Harper/Shadow Thief/Neverwinter Nine at the end, with choices publicly opposing Neverwinter, while privately undermining all its enemies. Due to a badly-written ending, however, this actually backfires. Despite the Shadow Thieves being cell-structured and having only two people in town who know enough members to lead them, at least one of whom dies canonically if the player joins the Thieves, killing both somehow causes the Shadow Thieves to be stronger and better organized.
Rocks Fall, Everyone Dies: The ending. The REAL ENDING. No we don't know why either, but if you play the expansions it turns out you live.
While you can alter the dialogue in the Mask of the Betrayer expansion a bit, many of your companions can actually survive, with only Bishop, Qara, and Grobnar 100% confirmed to be dead, with Elanee and Casavir strongly implied to be dead but with room for ambiguity. Bishop and Qara usually die before the ending occurs, though it is possible for them to survive until the ending. Elanee and Casavir were not well liked and killing them off was probably done just to justify them no longer appearing and making way for the new love interests. A somewhat obscure conversation in Storm of Zehir indicates that Casavir actually survived, having merely been seriously wounded, but was captured by Luskan troops.
Zhjaeve is the odd woman out. It's never confirmed whether she lived or died.
Rules Are For Humans: Lorne has the Deathless Frenzy ability from the Dungeons & Dragons version of his "Frenzied Berserker" class. Players can also become Frenzied Berserkers, but never get Deathless Frenzy.