The file system/partition sceme is very similar to Windows...
different filing system scemes, of course. Linux can't use NTFS, but has several to choose from. Ext3 is a safe bet.
Also Linux uses a seperate swap partition, unlike a swap file that is used in Windows.
Also Linux doesn't use C: D: E: drives or anything like that. Everything is part of a overall directory tree. Starting at / which is called "root". Every filing system (except swap partition) is mounted as a directory of that directory tree. It's makes for a much more transparent setup then what you get with Windows. For instance if you want home folders to be a from a remote file server and use it for many different computers, as a sort of "roaming profile" you just share it using NFS and mount it to /home/ and when people log in they have their home folder on that network share, and to them it's as if it's realy a local disk.
Same for floppies and cdroms even.
So what I like to do is have one big / (root) partition were most my applications go. Then I have a 1 or 2 of swap partition, and then a seperate /home partition. That way if I decide to change distros I can just format and blow away the OS, but still be carefull to keep my /home partition untouched. Then when I install a new distro all my user files are untouched. My user preferences and such can even survive intact between distros with no problem. (although going from version to a new version of applications can cause problems if the version that is installed is very different from the previous distros version).
The one caveat is that Linux displays user ownership using username and groupname, however it realy keeps track of it using UID and GID numbers, which may or may not be the same between each install. The fix is simple though. Before logging in as your user log in as root and issue a change of ownership command like such:
chown -R username:groupname /home/username
For instance I use the same name for my username and main group. So my command would go:
chmod -R drag:drag /home/drag
And that will fix the permissions so that your user can use your files with no problem.
Also user preferences are stored inside the actual home directory unlike Windows which has a universal single registry file...
These files are normally not seen because they have a . at the beginning of the filename. (also the shortcut ~/ is the wildcard that means /home/my.username) so to see these configuration files and directories you go:
ls -al ~/.*
and that will show all your hidden files.
So if any preferences get screwed up, delete the file or directory and it will be regenerated from defaults the next time you use your application. The only exceptions are stuff like Gnome apps that use a singular .gconf directory that it uses for most apps. Sometime you have to get creative...
Just becarefull with configuration directories for things like Evolution (e-mail client) or Mozilla/Firefox because you don't want to loose your bookmarks and saved mail files. Before screwing with their configurations backup their data you want to keep safe.
However keep in mind that your system-wide configurations are stored in the /etc/ directory. Be very carefull with those and back them up before editing them. If you blow them away they are gone forever and it can render your system non-functional. They don't work the same as user preferences.
So that way you can maintain your user directory between different system installs, and even different OSes. If you need to move them to a new harddrive or a different server you can simply wrap them up in a big tarball (linux equivalent of a zip file) and copy them over and untar it. Also any realy custom configurations you want to save, simply copy the text configuration files and keep them around to be copied between machines or into a new install (keeping in mind the differences between versions, of course Major version numbers usually indicate incompatabilities with older versions. Like for instance you can expect Evolution 1.0 stuff to work reasonably well with Evolution 1.4, but not with Evolution 2.0), but that's usually not worth it unless you put a lot of effort behind specific configurations.