I backup my PC on a nightly basis and one of the directories I grab in my backup is my APPDATA directory (%homepath%\application data), in my opinion what PHPEd is missing most is a directory to store all the settings in this path. This is beneficial for a few reasons:
1) User independent settings, the way it is now (from what I can see) everyone shares the same settings, not that it's an issue for a single developer but if the same machine is used by different developers then they must use the same settings or have a hybrid of each other's settings.
2) Easier for people like me that want to backup the settings to a program that is important in day-to-day operations and at least for me setting up PHPEd the way I like it is something that takes me at least an hour.
Also, I read in another post you also store registry settings, not refraining from it entirely is cool, but it'd be nice if the config file format was somewhat like filezilla where it stores all settings in a file, this just makes it easier to restore from a backup (given you have the same directory structure wherever you're restoring, ie. in the event of a system crash or a reformat).
This should really be considered for future versions, great product