There's been an experimental feature in the works under chrome's about:flags page called Multiple Profiles, which may eventually do what you describe, though it

There's been an experimental feature in the works under chrome's about:flags page called Multiple Profiles, which may eventually do what you describe, though it's still under development so you aren't able to turn it on yet: Multiple Profiles Associates every browser window with a profile, and adds a profile switcher in the upper right corner. Every profile has its own bookmarks, extensions, apps, etc.