Linux: 21 million
FreeBSD: 17 million
I was surprised to find Linux bigger when it's only a kernel while the FreeBSD repository also includes the FreeBSD equivalent of GNU coreutils and all the BSD init infrastructure and stuff. I bet this is the outward reflection of what people are seeing when they say FreeBSD has the better architecture.
I'm really curious to know if Windows and Mac are bigger or smaller than open-source operating systems. Of course a direct repository count probably wouldn't be fair because their repositories probably include their built-in desktop environments and stuff.