I use the digital clock the most, but the steps counter comes a close second. It is really useful when I have to measure 100 steps to recharge the battery for the VS seeker, especially in areas that distance and steps taken are hard to measure (like the blizzard area and the open water).
The application I can't stand, though, is the dots one. I don't get the purpose of it, and I really want to return the screen to what it was when I started it so I can start a new pattern. Forgive me for not checking back on the thread to see if anyone asked and answered a question about it, but can someone explain the dots application to me? You know, the one where all the dots clump together as you move the stylus over it?
I use the happiness checking guide, I'm not sure if that's the name, but the one where you click the Pokemon and it shows how many hearts it has. I also use the digital clock as well. I use those two the most.