Don't know if this has been "documented" somewhere or is just widely known anyway, but here goes.
The new keybinding UI has nicely separated categories, and you may have your own for your addon's bindings. Just specify the category attribute on
each binding to be included in the category. It will load a global or a string, like some other XML string attributes. Custom categories are placed at the bottom, above "Other".
Code:
<Bindings>
<Binding name="MYADDON_COMMAND" category="My addon">
ToggleFrame(MyAddonFrame)
</Binding>
</Bindings>
You may also combine it with the existing header attribute.
Personally I hope people won't use their own categories if they only have like a coupla bindings, though.