Famitracker is a NES composing program. It was originally a monolithic cathedral project written by jsr without a Git repo. There were several forks made, including HertzDevil's 0CC-Famitracker which had a Github repo and added features. Famitracker's creator released a "beta" without source code, then abandoned the project. 0CC-Famitracker reverse-engineered the binary to merge in some features. I maintained a "bugfix patch-set" on top of 0CC for several months, but kept running into merge conflicts, so I ended up forking an older revision of 0CC, calling it j0CC, because 0CC's maintainer was adding bugs and refused to accept contributions (including bug fixes). Then we both abandoned our forks...
libgme is a library which emulates game-console sound chips, and is used in media players. It was originally written by blargg, but now has 2 active forks: A "linux" fork packaged in many Linux distros (including Ubuntu/Fedora), currently lightly-maintained by mpyne (which suffered a security vulnerability), and a "windows" fork used with foobar2000 (also builds on Linux via qmake) maintained by kode54, which is more ambitious with changes, including a slow but accurate SNES SPC700 emulator written by byuu and not affected by the security vulnerabilities.
I heard Amiga emulation (UAE) has multiple forks too, and WinUAE is more popular?
I would prefer if the forks had never happened, but it's not going to happen.
Many projects have research branches, integration branches, stabilisation branches, vendor branches, branches run by people with platforms or use cases not well served by the canonical branch, etc. But those examples are all either feeders for a canonical branch, or derivatives of it.
Are there any projects where there are multiple branches right at the top?
The closest i can come is in the various distros' versions of ancient common unix utilities, which are no longer maintained by their original creators. Distros will make fixes to them, and may exchange fixes, but there is no shared upstream. However, that is really a case of there being zero canonical branches, not more than one!