I can't believe that nobody else else has posted the most important real company that appears within the LEGO City theme... the LEGO company itself!
There is a good list of promotional sets on Brickipedia, that includes the set theme. Many of the town / city sets include logos or brand names of real-world companies.
Other sets that include real-world brands (some of which don't count as Town / City, according to the Brikipedia themes list) include:
- Esso appeared on some very early sets.
- DB (Deutsche Bahn) appears on various trains, including 7725.
- Sports sets such as, 3432 which has NBA logos on the player's chests, or 65221 that included a Spalding basketball.
- 1656 Viking Line cruise ship.
- Interfrigo, set 147.