1) A Grass/Fire/Water combo in every team I use
2) I like to track down every single item on a route or in a town, even if I have no need for them. My bag is usually full of junk I'll never use by the time I reach the fifth or sixth gym because of this.
3) When I get all of the HMs (or their later generation equivalents), I fly back to my house in the starting town, work my way back through the region and go through all of the HM areas that were inaccessible before.
4) Battle every single NPC trainer on a route. I shall not leave a route until all have faced the overpowering wrath of Me and the Boys.
5) On that note, I treat my Pokemon like I would a beloved family pet, I get attached to each Pokemon and get sad whenever they're defeated in battle, so every time one faints I'll always do something to get its happiness or affection level back up, take it to the NPC who does massages, level it up with a Rare Candy, play with it in Pokemon-Amie/Refresh/Camp, just as a way of saying "I'm sorry you went through that, you're a valued member of the team and I'll do better to make sure you're safe and happy."
.........Yeah, can you tell I have no social life?
6) When I've come to the end of a playthrough and done everything I want to do, the last thing I always do before deleting the save file is return to the starting town, walk back into my house, speak to Mum one last time (even if she just says the same thing every time you talk to her), and go back to the exact place in the house where I started the game, so it feels like I've come completely full circle.