Do bosses or boss encounters respawn?
I've been trying to farm Wilhelm, but he doesn't appear after beating him initially. Do I have to be in Vault Hunter mode to farm him, or is this just a bug for me?
Bosses do respawn, so yes. The quickest way to make this happen is to save your game, quit to menu and continue from where you left off. Certain maps, such as the Vault and Terramorphous' lair even spawn you right inside the map where you left off; this might also be the case for End of the Line.
I've been visiting End of the Line on playthrough 1 after beating the story mission related to it and Wilhelm was there waiting to kill me - he definitively does respawn.
Yes, I've killed Wilhelm multiple times. The first time I was alone, then I joined a group game and the group happened to be playing that mission.