This would actually fall under trademark. Works are copyrighted. Names are trademarked.
Saying "Superman" in a Spider-Man comic would be using a trademark. Having Superman actually appear would be using something that is copyrighted.
If someone where to use a building (to use from the example, a McDonald's), then the building itself can be copyrighted. However, depending upon the purpose, amount used, and whether it dimenishes the value of the original work it would fall under Fair Use.
Trademark is a lot harder to infringe upon than copyright because it exists for a completely different purpose. Trademark is used to identify something as belonging to a company or otherwise seperate for other things. DC Trademarked Superman so that other companies can't go around naming other things Superman and tricking DC Superman fans from buying items that have no real relation.
Maybe if you argued that Spider-Man referencing Superman confused readers into thinking that Marvel owned Superman there could be an issue, but I think that's unreasonable.