Top five:
1. Party checker. (I have two Pickuppers in my party all the time.)
2. Daycare checker. (...)
3. PokeRadar app. (Chaining...)
4. Happiness checker. (To know when I have walked enough for Return to have max power.)
5. Pixel Art or Color Change (Pixel art is fun, once I made a Houndoom =P And I like to change the colors, even though it is usually on red.)