In this roster I've tried to gather the Clone Commanders that appear in the movies. I know most of you will be familiar with their names, but their numbers and divisions can be handy to remember as well. Thus I have also added their proper Divisions / Squads / Corps / etc ...

Don't forget that at the beginning of the Clone Wars, color indicated rank. When the Phase II armor was introduced, color indicated their allegiance to a certain corps, division, etc ...

Phase I Armor (AotC):
- Clone Commander: Yellow
- Clone Captain: Red
- Clone Lieutenant: Blue
- Clone Sergeant: Green
- Clone Trooper
- Clone Pilot

Phase II Armor (RotS):
- Clone Marshall Commander Gree CC1004: Killed on Kashyyyk
- Clone Marshall Commander Cody 2224
- Clone Marshall Commander Bly 5052
- Clone Marshall Commander Bacara 1138
- Clone Marshall Commander Neyo 8826
- Clone Commander Appo 1119: Killed on Kashyyyk (in 'Dark Lord')
- Clone Commander Thire 4477
- Clone Commander Deviss CT-65/91-6210 (does not appear in the movie)
- Clone Commander Davijaan / Odd Ball
- Clone Captain Jai'galaar (Jag) CT-55/11-9009
- Lieutenant Galle
- Clone Sergeant Fox CT-0000/1010: Unknown what Clone Fox really is. He's the one who lets Bail Organa go after Zett Jukassa has been shot.
- CT-57/11 9048 Jag's Wingman
- CT-3423 Neyo's Lieutenant: Right Clone
- Captain Fordo Alpha-77 (ARC-77)
- CT-43/002

- Clone Airborne Troopers
- Galactic Marines
- 41th Elite Corps Kashyyyk Armor
- 41th Elite Corps Coruscant Armor
- AT-RT Driver
- Hawkbat Battalion

Unnamed Clones
- Members of Clone Flight Squad Seven
- Lieutenant of Commander Gree: Killed on Kashyyyk

Corps / Battalions / Legions / etc ...:
- 9th Assault Corps: Kashyyyk / Luminara Unduli & Gree
- 41th Elite Corps: Kashyyyk
- 7th Sky Corps: Utapau / Obi-Wan Kenobi Cody
- 212th Attack Battalion: Utapau / Cody
- 2nd Airborne Company (7th Sky Corps): Utapau
- Parjai Squad (2nd Airborne Company): Utapau
- 327th Star Corps: Felucia / Bly
- 21th Nova Corps: Mygeeto / Ki-Adi-Mundi & Bacara
- 91st Reconaissance Corps: Saleucami / Stass Allie & Neyo
- 501th Legion: Coruscant / Appo
- Shock Troopers: Coruscant & Mustafar / Thire
- 127th Gunship Wing: Geonosis
- K Company (Devision 327th StarCorps): Orto
- CloneFlight Squad Seven: Davijaan
- Muunilinst 10: Muunilinst / ARC Troopers with Fordo
- Clone Trooper Combat Engineer
- Clone Trooper 442nd Siege Battallion: Cato Neimoidia
- Clone Trooper Fifth Fleet Security
- 187th Legion: Mace Windu's purple Clones
- 7th Legion: Senior Clone Commander A'den, part of the 327th Star Corps.

Comics
- Faie 41st: Kashyyyk
- Keller: Toola
- Alpha-17, otherwise known as A-17 or simply Alpha

Appendix: Command structure of regular forces
- Grand Army: All armies, a total of 10,000,000 troops, with Supreme Chancellor Palpatine as commander-in-chief.
- Systems Army: 2 Sector Armies led by a High Jedi General
- Sector Army: 4 corps led by a Senior Jedi General (Jedi Master)
- Corps: 4 legions led by a Clone Marshal Commander and Jedi General.
- Legion/Brigade: 4 regiments led by a Senior Clone Commander and a Jedi General.
- Regiment: 4 battalions led by a Padawan Commander.
- Battalion: 4 companies led by a Major.
- Company: 4 platoons led by a Captain.
- Platoon: 4 squads led by a Lieutenant.
- Squad: 9 troops led by a Sergeant.

Source: Guide to the Grand Army of the Republic in Star Wars Insider 84