I enjoyed the last in-game terminal quite a bit, because it seemed to directly hint at the return of the Didact in Halo 4. That gave me chills. My favorite terminal is probably from "Keyes", though, because it's definitely the most dramatic and well-executed terminal in the game. It has little bearing on the story, but it adds a lot of gravity to Keyes' fate.
I also enjoyed the hidden last terminal, simply because it linked Combat Evolved to Halo 2 nicely. I never really envisioned the "heretic leader" (I forgot his name) meeting Guilty Spark in any specific way, so it was nice to see how that played out.