I've setup my mechanical layers how I want them... is there a way to save this as a default so all pcblib & pcbdoc files use this scheme?
I suspect not (anyone who knows better??). Layer names are another one of those poorly programmed not-objects. Also changes basic commands, e.g. OnLayer('Mechanical 13') becomes invalid.
I just leave them default (unnamed, except for inner layers which I usually shorten to something handy e.g. 'GND', 'VCC', etc.). Then it bothers me when importing other boards (e.g. from PADS) and all the names are automatically different...
Also nowhere in the documentation that suggests that layer names can be changed, or if there's a comprehensive way to do it, or reset them, or...

Tim
I think you can just save your .pcbdoc file with your customized layer names in some convenient location.
It is saved as a .pcbdoc but really is just a template file for future projects.
Next time you want to use this layer structure you just open the template as a pcb and then save it with a new name in your project.
Seemed to work fine for me.
... is there a way to save this as a default so all pcblib & pcbdoc files use this scheme?
It can be done with a small work around.
Save all the layers exactly how you want them in an empty project.
Open this empty project & save with a new name whenever you begin a new design.
There's a user script example out there that will save and restore layer settings. I ran across it a while ago and tried it out, but annoyingly the path where the settings are saved and recalled from is hard coded. I tried to modify it to be able to browse for and select a file only to find that the Delphi functions to invoke a save/open dialog crash Altium--which I guess is why the path was hard coded

I belive this is the one:
http://wiki.altium.com/pages/viewpage.action?pageId=11240008
There was a script available for earlier versions of AD, but the compatibility broke somewhere around AD14. Tried to rewrite it but it only worked for mech layers 1-16, not 17-32. Now I use a template PCB file instead.
PCB template file is the way to do this!
1) create empty PCB, change everything as you like (this includes rules, layers, PCB options, size etc). I even have a few special "project parameter strings" placed, like ".ProjectTitle"
2) save it as some "myPCBtemplate.PcbDoc"
3) change settings in "new PCB document template" to point to that file.
from now on, each time when you click "add new to PCB project/PCB document" you will have the same nicely prepared setup