Comment 1 for bug 425938

As a work around:

For each web app, you can create a symbolic link to /usr/lib/chromium-browser/chromium-browser with a unique name (like "gmail"). And another launcher (see script /usr/bin/chromium-browser) which launches it, as well as specifying --user-data-dir and so on. Then, create a desktop file which points to the new launcher.

This will cause Do to think its a whole seperate program and will use the .desktop's icon and will not group it with existing chromium windows.

I imagine something similar could be done with prism/wine/etc until a better solution comes around..