Im going to be quite general and give you the top 10 most used in each tier. 1 is the most used, 10 is the 10th most used. Note: the order may be a little inaccurate but generally if it is wrong it's the same Pokemon with a slightly different order. These are stats from october so don't yell at me in the comments.
Ubers
1- Primal-groudon
2- Xerneas
3- Arceus
4- Darkrai
5- Mewtwo
6- Kyogre
7- Greninja
8- Ho-Oh
9- Yveltal
10- Salamence
Overused
1- Talonflame
2- Heatran
3- Scizor
4- Landorus-T
5- Rotom-wash
6- Garchomp
7- Charizard
8- Skarmory
9- Gengar
10- Ferrothorn
Underused
1- Salamence
2- Swampert
3- Donphan
4- Crobat
5- Hydreigon
6- Forretress
7- Beedrill
8- Nidoking
9- Chandelure
10- Empoleon
Rarelyused
1- Hitmonlee
2- Exploud
3- Alomomola
4- Flygon
5- Banette
6- Meloetta
7- Rhyperior
8- Sharpedo
9- Hitmontop
10- Tyrantrum
Neverused
1- Audino
2- Lanturn
3- Drapion
4- Magmortar
5- Golbat
6- Sandslash
7- Rotom-C
8- Registeel
9- Malamar
10- Gurdurr
Note: From experience I would also worry about sawk, scyther and mismagius.
PU
http://www.smogon.com/smog/issue37/introduction-to-pu
https://docs.google.com/document/d/1rk_LTrme-tsH4XNhl1SuAfsMEPfHYMz23ZZo3ySQyHY/edit?usp=sharing
I couldn't find any usage stats, but reading this will help a lot, consider Pokemon listed there threats in PU.
Little Cup
1- Mienfoo
2- Pawniard
3- Fletchling
4- Spritzee
5- Chinchou
6- Staryu
7- Drilbur
8- Diglett
9- Abra
10- Timburr
I hope this helps you in your future endeavors.
Source: http://stats.pokemon-online.eu/past-stats/october-2015/
