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Pedometer when I'm hatching eggs, Counter when I'm EV training, Itemfinder when I'm exploring a new area, and the Analog Clock when I'm not doing any of the above.
Well. I like the Marking Map. It helped me a whole lot trying to catch Mesprit yesterday (YEAH, YESTERDAY!!!). It is a very good improvement, comparing to how weary it was to find Latios/Latias in R/S/E and the Legendary Bests in G/S/C.
The Dowsing Machine in the Pokétch is handy as well. Now you have to choose only between registering the Bike, a Rod and the VS Seeker.
The Pedometer is helpful for breeding and evolving via hapiness! The Friend Checker also works for the last case.
I recall using both the Coin Flip and Roulette apps frequently. Although they were both created for frivolous uses, I tended to use them for decisions or to determine things by
pure chance. The step counter was also quite useful when accessory hunting in Amity Square.
I love the day care app so I know when an egg has been made. But, I also like the step counter app and chaining app for chaining shinies. I would have to say my favorite is the color changing app though, it's nice to be able to change it since I got tired of the default green after so long. >_>
Day Care app, so I don't need to wait like a day, then realize the egg has already been hatched. I use the step counter for my own entertainment, as it tells me how many steps I've taken since I got the Poketch.