TrueCrypt encrypted containers can be formatted as NTFS or FAT file systems.
I haven't tried other file systems.
I can add ext3 to the list of filesystems known to work with TrueCrypt, useful for apps such as Nautilus and TightVNC that create files with colons in their name.
Also, although this is slightly off-topic, you can easily store a Linux home directory and mount it in place, i.e. just one big volume in /home/username which you can mount with
$ truecrypt -t volume.tc ~
and the full home directory replaces the previously empty directory.
The OP is asking for something similar on Windows but that's much trickier on NTFS and Windows for a variety of reasons - TrueCrypt still doesn't allow mounting at a junction point, and a directory used for this purpose must be empty, and by the time you've logged in, you've already got a lot of files open (e.g. your registry hive).