Would it be possible to get a popup asking something like "This file is read only, would you like to make it writeable?" when attempting to edit a read only file?

I know I can change this in the file properties, but it takes a bit more time. Also I could just change all of the file attribs, however as TFS is being used on this project and they have been using Eclipse (How I hate that app). Anyway, one of the ways TFS tells if a file has been edited is the read only flag. So going in and mass changing all files in the folder structure isn't a good idea for us.

Not a big thing, but would be nice if you would consider it in a future update!

In some cases, files controlled by Source Control Systems are made readonly on purpose -- such as locking them from being edited. If you want to break them, the easiest way is it clear R/O flag.
Perhaps you can find a setting in that IDE that would prevent it from turning R/O on?

Yeah, I've looked into that and unfortunately there is no way to clear the flag automatically.

What I've been doing is using PHPEd for all of the file editing and using Eclipse for the TFS and project packaging (it's a proprietary thing). So it's just a pain to do and such a popup allowing me to quickly clear the read Only flag when attempting to edit a file. Otherwise I have to clear the flag manually or do the entire folder, neither of which are all that desirable of a solution for me.

You can write a simple script that will clear the attribute (or perform anything else with the file), register this script as a command in Tools->Settings->Integration and bind a shortcut to the command. So clearing R/O will be just a matter of pressing shortcut.