One of the lovely artifacts of web project not having project files is that the contents of the project are determined by the contents of the directory. Oh happy day. This feature has caused more problems in a collaborative development environment than the problem of the project file being locked checked out by a single control-mongering developer.
One of the gotchas you must be aware of is that when you try to check in your files via the Check In option when you right-click on the Solution Explorer, Visual Studio.NET will very often try to check in the contents of your BIN and OBJ folders. Once this is done, the next time you get latest from source control, the project won't build because the individual .DLL files are set as read only.
So how do you get around this?
You can either use the View Pending Checkins context menu instead of going directly to the Check In window. The pending window will give you a tree view of all files checked out. All you have to do is un-check anything in the BIN or OBJ folder.
The other option you have available to you is to use project files with ASP.NET 2.0 applications . There is just a little work integrating this solution into an existing application.