First I want to thank you for this plugin - I was looking for something like this, and haven't noticed any bugs in the recent development build (#7).
That said, I have one (or two) suggestions:
A feature to let signs/plates/portals/etc. teleport you to a warp instead of fixed coordinates would be nice. That way, you wouldn't have to change the destionation for each sign/portal linking to a specific location whenever it's coordinates change (because somebody build a new house at a new location, you rebuild and the door is somewhere else, etc.).
Even better, while breaking out of the scope of "portals", would be custom command(s) that could be run instead of teleporting the player. While there is (Better)CommandSigns, this would have the bonus of not being limited to signs and already having the custom portal mechanic (additionally, BetterCommandSigns does not seem to work at the moment ). That way, you would gain more flexibility: you could, for example, use Nucleus' Warps instead of PJP's or set a players gamemode prior to warping him.
Just an idea for you to think about