I'll start with a few. Feel free to add any that may have irritated you during your FNV experience.
- If you happen to be scavenging Fiend territory and you run into Vault 3, you might be able to enter without the Fiends being hostile if you pass a speech check. You might wanna kill everyone anyway if you're looking for items and such, but maybe you should wait. Diane, at the Red Rock Drug Lab has a quest that involves Motor-Runner, the leader of the Fiends. If he's dead you can't do that quest, and therefore you cannot learn the Khan Trick from Jack.
- If you clear out Quarry Junction, find Melissa and do her quest, you can't finish the main quest for the Great Khans (Oh My Papa) back at Red Rock Canyon because she disappears from the game.
- If you visit Novac and speak with Ranger Jackson, you can learn an unarmed technique if you visit Ranger Station Charlie for him. Once you've learned the technique, you can't speak to him again. This is unfortunate because you need to be able to talk to him for Raul's companion quest, Old School Ghoul, which is now impossible to complete.
- After completing the quest, The House Always Wins III, you'll get a warning from Caesar and the NCR to stop working the Mr. House if you want to continue to work with them. I would recommend making a save here because if you complete The House Always Wins IV, all your quests with Caesar or the NCR will be failed and you can't change your mind.
Add in any instances in which you accidently/unknowingly broke a quest that you didn't want to.
P.S. I apologize in advance if some people misinterpret this as another thread full of glitches and complaints. I'm a huge fan of the game despite the issues, although I do hope the next patch for PS3 and XBOX 360 will clear up some of these problems. I'm just trying to create a thread for the people like me, who can read through it before starting a new character and keep in mind some facts about the game's plot that might help them avoid upsets or frustration. Finally, if this has been done already just post the link.