From what I have seen, they look absolutely similar and their functionality are pretty much the same.
See the attached image:
Gnote is a port of Tomboy to C++.
Pros: Faster, smaller memory footprint.
Cons: (Still) No synchronization support (e.g. Ubuntu one), which is a dealbreaker for most people.
You can read about the author's motives here.
It is the same note taking application, including most of the add-ins (more are to come). Synchronization support is being worked on.
Tomboy is not going to be installed by default in Ubuntu 12.04 - I suppose Gnote may take its place some day.