His Kree-Skrull War in the Avengers was a favorite of mine. He had a hand in launching "The Defenders" which is one of my favorite "non-teams" in history, and (if memory serves) he launched the "What if" series too! I also enjoyed his stories in the Invaders and the All-Star Squadron. He had a knack for writing characters with a Golden Age feel, but his stories were also a bit quirky and off beat (which I love). How's that for a short list?
I'm a fan of the Kree-Skrull War, too, but I think the forming of the Defenders was a top idea. It worked so well for the heroes involved and built some great continuity.
Thomas did write the first two issues of What If...? What If Spider-Man Had Joined The Fantastic Four was one of the first back issues I ever tracked down.