Actually, FogBugz is trivial to scale - there is never any more than a few dozen, to hundreds of users for any one project.
And Copilot wasn't even envisaged or created by Joel, but was rather a project created by some interns.
FogCreek doesn't innovate (they have a bug tracker and a remote support application based on VNC). Joel just happened to be one of the first to blog constantly about technology. He doesn't even allow comments on his posts because he doesn't want to have to deal with people contradicting him (not that he doesn't do an excellent job at this himself).
There are so many great developers and businesses out there that you could use as an example to model your business and software on. Use them, not Joel. Let Joel's business and opinions fade away as other smart, innovative companies run rings around his ageing product suite.