Yeah, I know it's confusing, which is why I want to straighten this out on my resume. Unlike working for IBM/Accenture/etc., where as an employee you may be assigned to work on site for their project with Government Agency XYZ, my situation is much different.
Imagine that Government Agency XYZ needs 100 employees for their IT department. XYZ can fill 50 spots with federal workers, but needs to fill the remaining 50 spots (the reason for this gap is largely because the market salary of IT workers is higher than that which they would receive via the standard Federal Government pay scale). To fill these spots, several contracts are made with local companies to provide the [50] employees.
Effectively, these 50 contractor employees (of which I am one) are day-to-day exactly the same as the federal workers at XYZ. They have XYZ email accounts, they are on-site with XYZ 100% of the time, and usually they are with XYZ for multiple years. The only tangible difference is payroll; at times I'll joke "I work for XYZ but my check comes from Company C".
The reason I want to highlight Agency XYZ on my resume over Company C, is because:
1) Agency XYZ looks a bit more sexy IMO
2) While working for XYZ I've been associated with Companies A, B, and now C - focusing on the companies rather than XYZ would imply [on paper] that I've switched jobs twice.
However, as I mentioned, I'm now doing some extra work for Company C that I'd like to highlight, and as riverripper stated, it would be "highly uncommon to have any US government position listed as doing work for a private employer". I think what I'll end up doing is using a heading of "Government Agency XYZ via Company C, Inc." and then having a small sub-section after my XYZ accomplishments that highlights my additional Company C accomplishments. Companies A and B will just not be on there for sake of simplicity.