My favorite part of Fallout 3 was actually probably President Eden, now that I think about it. Malcolm McDowell had the perfect voice for a bombastic statesman, his broadcasts on the Enclave Radio station were great, and the reveal in Raven Rock was a really neat twist. I also liked the Tranquility Lane quest, because it created a new context for Fallout's idealized version of the 50s so they could take it in some interesting directions. Those are certainly the most standout parts in my memory, from the main plot at least. Liberty Prime was also pretty cool, but just in a 'I'm walking beside a giant fucking robot that's tossing nuclear missiles' way.