There a few a few 1 base = 1 company sets out there, but generally the companies are grouped into battalions etc.
My RKKA Brigade Commander is based on Tim Gows NATO Brigade Commander, and although the elements and combat resolution are at company level, the companies manouvre as part of battalion sized formations. There are some aspect of the combat model I’m unhappy with, but I didn’t want break Tims system too much.
NQM, PanzerKorps and Piquet FOB have already been mentioned, another one to look at is Lightning War by Phoenix games (although, again manouvre is by battalion).
Great Battles of WW2/Dropzone by Bruce McFarlane also use company sized elements but then launches off into a series of multiple Corps sized battles better fought with Megablitz et al!).
Combat 300 by Ian Drury uses rifles companies as the infantry element, with tank platoons. Aimed at brigade sized actions, it works rather well imho. Published in the WD Journal. It is also aimed at using Kallistra hexes though.
I often treat Memoir 44 as having company sized elements, if you have a poke around on my blog you’ll find Memoir 45, my mods to make it fractionally more ‘realistic’.
"Mistakes in the initial deployment cannot be rectified" - Helmuth von Moltke