However if I do this then the WBStartup directory under system would be pritty much useless right? I could put any application I want to run from startup in the User-Startup file!
That's about the size of it - but the WBStartup drawer does things as if you had double-clicked on the icons, which means that the Tooltypes get parsed, which does not necessarily happen when you launch things from scripts. You sometimes need to add keywords like QUIET etc.
How do I go an create a script file? Are there any examples anywhere (maybe already on Workbench)?
Use a text editor, type something, save it.
Then look at the protection bits (Icon Info stuff, or shown in file-listers). If it has the "s" bit set then it's a script. If not, you set that bit, now it's a script.
Ed: there's a little more to it, but not much. The "rwed" bits have some relevance, particularly the "e" bit. If that is NOT set then the file is a project (which might be a script, might be data, or almost anything) and the file is NOT "Executable" by direct clicking on it, or naming it, etc. You have to type the command "Execute scriptname" in that case, this overrides the protection bits status.
If the "e" bit IS set then you can run the file/program by clicking on it or naming it, but that doesn't make it a script even though it could well be one.
It is the "s" bit that says "script file intended to be used from the Shell/CLI" and if it is also "e" set then you can call it by name and it gets executed as if it were a regular program.
