After playing through a Pokémon game, we often have several Pokémon that we grown to love and appreciate as team members. I personally always keep mine, and have dozens of boxes filled with them. What do you do with your Pokémon after you are done using them for a play through? Why? How many Pokémon do you have saved up from this?
I usually just either keep them in my party until I need to transfer them to the next game, or, if I'm starting a new game on the same cartridge, I take the main six or so Pokémon I used and stick them in a PC box after I start the new adventure. I've probably saved up a good 18-24 Pokémon that way, plus way more for the Pokémon I didn't really use but kept anyway because they would be great for trading and/or bragging rights
I always keep my Pokémon stored in my copy of Pokémon Stadium 2 for the N64. (I hope I can find a way to get another game so they can adventure again; it`s been so long since I last saw them...)
Wow, that's old school. Sadly, there's no method to get Pokémon from Gen 2 into newer generations, so there will always be that divide. Me, I tend to keep them in that their original game. My Sapphire, Pearl, and forward are all still in their original cartridges, with the exception of some AlphaSapphire in Bank. One day I'll get around to migrating everyone forward to Bank to live with me forever... but not this day!
I keep my main party members with the cartridge I fought with them on. I usually never reset a game so I always have them if I choose to return to playing that game. I don't transfer them to a new game because I want a fresh start and don't want to use the same Pokémon in a new adventure. I always want to branch out with different unique Pokémon.
I'd usually reset and play again, but I regret doing that without having some method to store previous Pokémon. Since gen 6 and Pokebank, I'd store teams in the bank and then reset. In OR/AS playthroughs I use DexNav to find high IV Pokémon so I can super train them on the spot, steamroll the game, and then upload the final team to one of my "Legion" boxes in the bank. My Legion is competitive. I almost have one box full!
Most just end up in boxes as I continue to work towards one day reaching living 'dex status. The Pokémon that I actually use in my team, on the other hand, I'll cycle between for post game content on new games. I usually only end up using a few of my favorites mixed in with my team from the most resent game, though.
Honestly, nothing. I just leave them in their usual position and probably don't touch the game again. I can't transfer them to any game, as I play on an emulator.
I send them either to the bank or another game as I restart most games again pretty quick due to being addicted to Nuzlocke runs.
I send them all forward to the bank to aid in my quest for a complete living dex. Now if I finished a pokmeon run, I would replace the old Pokémon in my livingdex with those fresh from the game, as the game ones probably were iv breed
Keep raising the main team until it's level 100, then I shove them in a special section of the boxes, for use in battles and to transfer up to the next game when it comes out.
I switch them over to the next Pokémon game. Not all, but all the good ones (Shinies, Starters and Pokémon which won't be obtainable in the next game)
Box them and forget about them, usually. I usually wind up buying both versions of the game - I have excluding Gen VII, anyway - so I often keep one file for Pokémon I want to keep, and another I can play whenever. I like having living dexes.