[tomwheeler]

I suppose I'm stretching the definition of SaaS here, but I'm going to say SSH (both client and daemon).

It was originally released as freeware, but after it was widely adopted in the mid 1990s, its creator made it proprietary and created a company called SSH Communications Security to sell it. After a series of security vulnerabilities in that commercial software, OpenBSD developers got fed up and created OpenSSH, and basically everyone migrated to that within a year.