I believe the XOR patent was the first major one, and certainly the most blatant troll – it hit most of the industry for a technique which had been described a decade before filing – but the software patent mess started arguably in 1981. Wikipedia has timeline of the evolving caselaw:

http://en.wikipedia.org/wiki/Software_patents_under_United_S...

It's also the patent that put Commodore out of business.