Beeminder: Personal accountability through commitment contracts. Helps me stay on track with my goals, often serves as a little extra "push" to do something useful even if I'm really low on willpower that day.

Anki: Maybe not underrated, but seems like it only really took off in language-learning circles. I create a card for anything new that I'd like to retain, and have been doing so for almost 10y now. Really multiplies the long-term value of sitting down and learning, since I can be relatively certain that I'll keep the knowledge with me for a long time. Particularly useful for papers.