Yeah Welcome Home is one of their best known songs. My Facebook display photo is me with the band's guitarist, Travis Stever. The other special thing about them is that all their music forms one complete story, all of which is based on a comic book the lead singer writes, which is called The Amory Wars.
Quick "best of" I'd recommend checking out, 2 songs per album:
Key Entity Extraction I: Domino The Destitute
Key Entity Extraction III: Vic The Butcher
Key Entity Extraction V: Sentry The Defiant
Number City
The Broken
This Shattered Symphony
Everything Evil
Devil In Jersey City
The Velourium Camper II: Backend of Forever
A Favor House Atlantic
Ten Speed (Of God's Blood and Burial)
The Willing Well III: Apollo II: The Telling Truth
The Hound (Of Blood and Rank)
The End Complete III: The End Complete
That was really hard to choose. There are so many awesome songs.
I also feel I should give a special mention to two more songs:
Elm Street Lover Boy - this is a song based loosely around the Nightmare on Elm Street movies, by Claudio Sanchez's solo project The Prize Fighter Inferno.
Deranged - written for Batman: Arkham City, a song from Joker's point of view and his thoughts about Batman.