I actually just developed an OCD a few days ago, organizing my pokemon according to various classifications... although some may be "forced" into those habitats to save space.
Lakeside/Riverside = consists of grass, water, and rarely even other pokemons that would normally live near the said habitat. Marill, Deerling, Stantler, Shaymin, Keldeo, Wooper, Whiscash, Basculin, Magikarp, Golduck to name a few.
Deep Sea/Ocean = consists of most water pokemon. This includes any water type that you literally should find in the sea/ocean. Some examples are Jellicent, Shellder, Corsola, Kingler, Tentacruel, Gyarados, Stunfisk, etc.
Caves/Tunnels = includes a lot of pokemon found in caves. Usually rock pokemon, but also includes other non-rock pokemon such as Golbat, Dunsparce, Koffing, Muk and Woobat. Basically, sewers are also considered tunnels, so..
Hot Zone = this includes pokemon that could live in extreme temperatures, or at least could produce those extreme temperatures. Since desert and ground pokemon (not placed in the Cave box) are very few, I've included all fire pokemon in the box(es) as well. Cacnea, Krookorok, Trapinch, Numel, and Sandshrew are found here.
Fields = this includes pokemon found in mostly any grass of patch, and does not match other boxes' quotas. Normal pokemons are most commonly found here, as well as some poison types found in grass such as Stunky, Arbok and Seviper. No need to give examples for normals you find in the field. There are at least two Fields boxes in every game i play. Flying types are also found here.
Forest = includes all bugs and even most grass types. Typically, all of them are found in forests, but not strictly. Bellossom, for example, isn't really a forest-exclusive... but since most of the oddish line are also found in forests, i've included bellossom here. Some exceptions such as Slakoth and Sudowoodo are also found here.
PowerPlant = All steel types and electric types. Scizor and Forretress are included in the Forest box, though.
Stronk/Strong = includes most legendaries and all dragons.
Party = mostly the ones i'm currently using for battles. Also includes the HM slaves.
Daycare = most "pink" pokemon are found here. Chansey, Clefairy, Wigglytuff, Granbull... etc. Not strictly daycare though, i just had nothing to name it. Porygon is found here.
Gloompit/Stinkpit = Includes a lot of dark and ghost types. Ice types that couldn't fit into the deep ocean category are also found here... such as Swinub (cave box is too full), Glalie, Delibird, and ugly Jynx.
Experts = Fighting and Psychic types.