Two come to mind for me.

This is just a strange moment. I had completed the game and went back in. Back in the tunnel before you come to the High Road area you come across the Tunnelers for the first time. Since I had already dealt with them they respawned. This time one showed up as "friendly" with a green marker just sitting there...until I used bangflash on his not so friendly bretheren. He became unfriendly very quickly.

A more LOL moment was going thru after completing the original. During the retracing in the first missle silo of the game where you get ED-E I had come across a living marked men and turned him into ash using the holorifle. Well a few game days later I went thru again since they respawn and have good loot. The ash pile is sitting there and I went up and saw it had something I must have missed before. I took it....while sneaking, since other enemies have respawned (this is right next to the missle where you first come across the schematic posters for "Red Glare") and.......I get a message...it states I have been caught pickpocketing and loose karma from stealing from a pile of ash.

Encountering the tunnelers or whatever they were called, for the first time