Sorry i hadn't checked back here in a bit. This topic in the forum has some good references as to what the different folders in the linux filesystem-tree are for: http://www.tomshardware.com/forum/236448-50-file-system-folders-purpose.
Anyways, here is a quick crash-course: Mountpoints in linux are a little different from the drive letters (like C: and D
in windows. A mount point is basically a location that you tell the operating system that you want to put your hard drive for access later. This is similar to designating your coffee table as a magazine area. You go to your coffee table and you find your magazines there. If you wanted to, you could designate some other place to be your magazine area like the kitchen counter or whatever. The same goes for mountpoints on the file system-tree.
Lets say for a minute that you are setting up Linux to dual boot with Vista and they both share the same hard drive. When you are installing Linux, you'd have to first make sure that your hard drive was split into two parts: one for the windows side and one for Linux. From there you need to split the Linux part into at least 2 smallert partitions. One part is going to be your swap partition which i spoke of earlier and the other will hold the operating system and everything else. You would tell the partition manager to put the file system on the swap partition to the 'swap' file system, and because it is a swap partition, it doesn't have a mount point: Linux will just automatically know how to access it and you will not be able to access it directly (as you shouldn't because it could mess things up). The other partition holds the entire file system and the OS and all its components and gets the mountpoint called ' / ' (without the quotes). ' / ' is the very top of the file system and it is where everything is stored. Think of it like a big folder where there are a bunch of subfolders inside of it to organize everything. You can't put anything outside of / because it is the highest level directory that you can get to.
Now, lets say you want to have access to your vista partition under Linux because it has all your music and you don't want to have a copy of all your music for both OSes. How do you get to that music? Well, you give your vista partition a mount point on your file system! Basically you find a folder that you want to go to when you want to access your vista stuff. If you really wanted to, you could create a folder anywhere in your file system and specify that as the mount point, but there are 2 folders that are dedicated by the file system to do this for you. These two folders are /media and /mnt. The /media folder is where temporarily mounted media (such as thumb drives and external drives) will show up when you plug them in. /mnt is the folder where your permanently mounted devices (think your vista partition) usually go. These functions are not set in stone as I have seen some distros only use /mnt and others only use /media and others use both, so it is up to you where you stick your vista partition. So, from there you specify a 'vista' folder inside one of those directories as your mount point, and when Linux installs, if you open a file browser and go to either /media/vista or /mnt/vista (depending on which you chose) you will find all your windows stuff!
It is important to understand that in Linux, there are no "Drive letters": everything is integrated into one big tree. In windows each drive letter makes a different tree with ' \ ' being the top of each individual tree and in Linux/Unix there is only one tree with the top being ' / '
If you are still a bit confused, don't worry, just experiment a little bit with live CDs and browse around the file system and you will begin to understand what I am talking about. The best way to get familiar with Linux is to just use it and try to immerse yourself if you can (just like learning a new language). By the time you are finished you will probably have a better understanding of what OSes are and how they do what they do, which is definitely a good thing!
Good luck!
-Zorak