One of the benefits of cross-platform software such as the Thunderbird mail client is that its often quite easy to transfer data from one platform to another. The data that Thunderbird creates (that contains your account settings, downloaded emails, mail filters etc.) seems to be identical whichever platform you run it on.
Under Linux, the data files live in "~/.thunderbird/". Under Windows 7, I found my settings in "C:\Users\<username>\AppData\Roaming\Thunderbird\". I suspect this location might move around a bit from one version of Windows to another. Searching for profiles.ini might be the best bet if you're trying to locate an existing installation.
So, once I had located the data files, all I had to do was mount the windows partition under Linux, and copy "profiles.ini" and the "Profiles" directory from the Windows location to "~/.thunderbird/".
You could also use this method to transfer your Thunderbird settings from one computer to another.