I'm thinking more in terms of production software, stuff like databases. If you want to license Oracle or WebSphere, you've got per-core or per-socket, per-concurrent-users, sometimes per-MIPS fees, may depend on field of endeavor, etc. Oracle and IBM are the masters of this particular art, but there are quite a lot of bits of proprietary software that include that kind of fee structure at least in part. Some game engines also charge you depending on your game's sales. A flat fee for any use, no royalties, seems limited to certain software niches, especially anything seen as non-enterprise.

So:

Would you prefer MySQL or PostgreSQL? ;-)

Here's a case of a BSD-licensed project overrunning a GPL-licensed one.