Okay, the exact answer is too long, and frankly, quite difficult to be 100% accurate. So I'll try my best and give an answer with as many details as possible.
They most commonly use Poison and Dark type Pokemon
First, let me list out some of the Pokemon used in almost all the generations:
Common to all Teams
- Zubat/ Golbat, with the exception of Team Plasma, who use Woobats instead.
Note: I won't be including temporarily controlled Pokemon, so sorry about that.
Team Rocket
- Ratata and Raticate
- Muk and Grimer
Now, from the duo, Butch and Cassidy:
- Primape
- Hitmontop
- Cloyster
- Mightyena
- Shuckle
- Raticate
- Houndour
- Tentacruel
- Sableye
- Granbull
And then, from the duo, Atilla and Hun
- Skarmory
- Muk
- Espeon (Note: Latios, temporarily. I said that I wouldn't mention temporaries, but a legendary deserves a note here)
From our beloved goofs, Jesse and James:
- Wobuffet
- Pumpkaboo
- Seviper
- Yanmega
- Arbok
- Shelder
- Dustox
- Lickitung
- Woobat
- Frillish
- Weezing
- Cacnea
- Chimecho
- Mime Jr.
- Cacturne
- Banette
- Carnivine
- Aipom
- Inkay
- Mime
- Carnivine
- Cacnea
- Growlie
- Chimecho
- Victreebel
- Yamask
- Amoonguss
- Weezing
- Gyarados
- Dustox
- Yanmega
And Meowth
From Giovanni:
- Persian
- Golem
- Kingler (2 of them)
- Mchamp
- Rhydon
- Cloyster
