My faves from the first album are Finding My Way, What You're Doing, Here Again and Before And After.
As far as Fly By Night goes (And The King can attest). Anthem, Best I Can, Fly By Night and parts of By-Tor And The Snow Dog (in the middle of Working Man) were played live before Fly By Night was recorded.
Portnoy even honored this "medley" on the Working Man tribute CD and I'm not having a brain fart I think Dream Theater also covered part of it during the Six Degrees Tour.