Mostly it has no effect. About the only place it might is for GPLv3 and for other licenses that have patent clauses.
For GPLv3, if you have a patent and ship software that includes that patent, then you have to provide a royalty-free license to that patent to all current and future users of that software - this stops people sabotaging GPL'ed software with patents.
Otherwise, if you aren't shipping the software, then the patent is yours and you can demand a license (hence the ... well, extortion pretty much sums up my feelings on the matter, of Microsoft vs the Linux community, regarding the 235 patents they won't give any details on - how can you stop infringing when you don't know what you're infringing?)
This is what software patents (though TBH, it's not JUST software patents) have turned into - a way to gather in money you don't deserve, or to restrict your competition.