Ah. So many great side quests in this game. I'm going to narrow it down to a few.
Superhuman Gambit, Stealing Independence and You Gotta' Shoot 'Em In The Head. Why?
Superhuman Gambit is an excellent example of just how campy and over-the-top Fallout can be at times. It's not out of the realm of possibility or too over-the-top. It's just fun with memorable characters and their "superhuman" identities. The design of the places you have to visit are very well-done, their hideouts being representative of the characters they wish to portray and being filled with their minions.
Stealing Independence is one that doesn't seem too unique, but it's special to me. I loved exploring the National Archives and that entire Mall area in general. The Museum of History, the National Archives, the Washington Monument, the Lincoln Memorial, the Capitol building. Sydney is likely one of the best written side characters Bethesda has ever created. She feels like an actual person in many aspects, fleshed out with her own holotape explaining the death of her father, her own unique 10mm submachine gun. She's not even essential either, so you can just kill her and take 100% of the reward for yourself. But why would you do that, you monster?
You Gotta Shoot 'Em In The Head is extremely fun and one of the largest, most quality-filled side quests in the game. It brings you to many of the strangest minor characters in the 3D Fallout games. And the most fun part? You can convince ALL of these characters to give you the keys without harming them, you can steal it from them and the cherry on the top? You can completely betray Crowley, take his key and go to Fort Independence for yourself, beat him to it after giving him the keys or just kill him outright. There's many outcomes for this quest and they're all extremely fun to pull off.