So, I only know of 2 quests that actually make a difference (Lock & Load, Things that Go Boom). Any other?
By difference, I mean that it actually impacts the story/world in a way.
If you do the above missions, in The Beginning of the End, Jack will moonshot 6 - 12 loaders to aid you in Vorago Solitude (including EXP Loaders). While if you don’t, he’ll moonshot only 2.