I don't think you can actually edit / write files on the iOS root folder (for better or worse). Probably due to permissions or the way that DOSBox works. I tried to copy and rename a file and got an error telling me to check the original paths of the files. (It was the AppStore icon.png file). I was just curious...
A reader commented on TUAW site that DOSBox does not allow write access, however iirc the Windows and OS X version does.
I tried running Dark Forces but it ran too slow. Opening the configuration file on the Mac it reads that core is set to simple. I'll play around with this later, but I'm sure I can get some fun programs running that will run decently. Still wondering if this will work with a Bluetooth Keyboard or an iPad Dock Keyboard. It didn't with the USB/Dock Adapter, but there's only one way to find out. However I'd guess No since it uses a 'custom' keyboard input and not the standard iPad pop-up keyboard.