Randall Clark's journals were great too, and I think they were one of the best things about HH.
This. None of the other tales and adventures in any part of the game or DLC's came close to the feelings I got from his simple, poignant diary entries, and finally finding his bones and drinking a toast to him at sunset with his bottle of whiskey (well aged). What this story accomplished, in the form it was presented, allowed you to truly see through one of the game character's eyes, and feel with his heart what he had felt, through all his years of loneliness, love, depression, joy, hatred, and abject hopelessness. They put a whole lot of life into a few random computer log entries. Granted, that kind of character building and storytelling is pretty hard to fit into the regular RPG encounters with living NPC's, to be sure. The written word will always be superior for evoking emotions and describing actual feelings, than anything that can be done in a graphical or video environment.
Worst sidestory? All of the Legion stuff. The whole premise that any right-thinking human being who isn't already a cold bandit or outlaw murderer/abuser type would ever deliberately join them and do their evil sneaky bidding, sickens me. If they had done more with them than made them a pretty unbelievable caricature of evil incarnate, and produced more and more interesting and better-written quests for that side, that might have been different.