The actual lawsuit in question here is the NFL's exclusive contract with Reebok for NHL merchandise. However according to CBSsports.com, the actual issue the NFL wants a ruling on is to declare itself a single business entity, instead of a loose collection of 32 separate business enterprises.
Essentially the NFL wants a permanent decision by the Supreme Court that would allow it to avoid all anti trust lawsuits.
If the Supreme Court rules in favor of the NFL, that they will be free to squash team relocation plans, merchandising deals, and virtually anything that the league doesn't agree with.