Hard Drive Setup & Maintenance
If it is a Windows only box, I like to have four partitions. The first one is 3 gb or so it is for the operating system only. The next one is usually 7 gb or so, just for programs. This is nice because if for many programs, those that don't need registry entries, you don't have to reinstall them when you replace your OS.
The third is for 'documents and settings' meaning all my music/movies/documents/preferences/desktop et cetera; it takes most of the available space. This is probably the most important parition to keep seperate from the OS. This way if Windows dies (as it has a tendency to do) you can resintall without losing your stuff. Lastly I like to have a 5 gb or so "slush" partition. I use bittorrent and it is messy. Meaning if you use it you'll have to defrag a lot more than otherwise; this way I only have to defrag a 5 gb partition rather than a huge monolithic one.
I realize four partitions is a lot for some people. This can be condense very easily to two. One for the OS & programs, the other for every thing else. Some programs you have to reinstall if you reinstall windows anyhow (any program with a CD key), so the programs partition may not be that big of a time saver for some (I only use free software when I have to use Windows so this works for 90% of the apps I use). The slush partition is only if you do a lot of downloading.
If you already have windows installed, don't despair. There are ways you can change the partition your 'docs & settings' folder is to. If you haven't installed yet, you can make an install disk do this and much more for you in an hour flat.
The other thing I do to keep my hard drive clean is I have a Windows VMWare image. So if I want to try out a new (unstable or potentially useless) program I install it on my Windows image. If the program hoses your system or if the program is worthless, just replace the image with a backup (presuming you back up VMWare images you use a lot). That way you don't have to fix anything if it was bad, and you haven't cluttered your registry - which seems to cause many of the problems Windows has.
VMWare is a company which specializes in virtualization, meaning their software makes your computer tell an install CD that you aren't running an operating system right now and to go ahead and install (even though it is installing to a file, not an entire partition). All this without leaving Windows or Linux. So you can have an operating system running in an operating system. This way if the one inside gets hosed, no problems, you haven't touched the outside one. VMWare released a free player as well as a free server. You are going to want the player in this case, and you can create a Windows image just fine with the free player.
To keep everything up, I schedule a virus scan of my slush partition every night. If your AV supports active scanning (meaning it automatically scans anything you download), you may not need to do this. I think active scanning is a waste of CPU cycles, so I disable it, but still run a limited scan fairly often. That way if I downloaded anything bad I catch it before it gets anywhere. The rest of my system gets scanned every week (or every other). I don't run spyware scans, they've never found anything but some cookies that get cleared out when I exit firefox. If you must use Internet Explorer, schedule some spyware scans.
I also run a disk check once a month. Just in case you know. You really don't have to defrag hardly at all with NTFS. I mean it won't give you a big performance boost really. If you are running bittorrent or something messy, I'd keep it confined to every other week at most (which is where the slush partition comes
I love Linux (in case you haven't noticed). I've used FreeBSD briefly, but this advice is aimed at Linux users, though it could probably be modified to fit a BSD. With a Linux-only box I use four partitions as well, though for different reasons.
There are a lot of good filesystems you can run linux on. There are some bad ones too (fat anyone?), but I'll only mention my preference. ReiserFS is a great filesystem. I used it when I was on Mandrake (oh about 9.0). Now though I am on EXT3. EXT3 may not preform as well as Reiser, but I've found a lot more tools for it. Most importantly the EXT3 windows driver is far more stable and functional than the Reiser one, in my experience.
The first partition holds the actual OS. Messing around with Linux I hose my system regularly, so it is nice to make a fix so easy. The second partition holds the /home directory, this is analagous to 'documents and settings.' The third holds the '/etc' partition, which is full of configurations I've made to different programs. The last is for the swap partition (kind of like a dedicated area for virtual memory). I don't have as much RAM as I'd like, so I use a swap of 512mb. It is rarely, very rarely, half full, but better to have it than not.
I run bittorrent too, so I could have a slush partition, I just never have. Four partitions is a lot so you can fairly easily use a single partition to hold /home and /etc, and one for the OS. Having a swap partition really is a good idea if you don't have more than 512 mb or ram, but you could always ditch that too.
This is a lot easier. I just schedule FSCK to run on each partition every month. Thats it!
Dual Boot Setup
I currently have a dual boot machine. I don't want 8 partitions on a single disk for it, I combine a number of them down to four total. First I have a partition for Windows. The whole thing, docs and settings, program files and the OS. If Windows dies I can always transfer stuff to my Linux partion (from Linux of course) easily. Then replace it when I reinstall Windows.
Next I have a small swap partition, 256 mb or so. My laptop only has 384mb of RAM, so I really need the swap. Third I have a 'slush' partition. I know it seems wasteful, but it is FAT32 so both Windows and Linux use it for BT traffic and other messy stuff. I have friends who used their slush partition for both the '/home' and 'documents and settings' sections of both Windows and Linux before too, which is neat, but large FAT partitions make me nervous. If you don't do that, since the slush partition is FAT32 you can read and write from both Windows and Linux. Which is nice, but that part is unecessary, there are EXT2/3 and ReiserFS filesystem drivers for Windows, so Windows can at least read what is on the linux partion. Every modern Linux distro has NTFS read support too.
Lastly I have my Linux partition. Everything under "/" together (unless you mescalate /home and docs and settings in the slush partition). That way if I hose Linux, I can boot into windows, using Windows EXT2/3 drivers I can save my /home and /etc partitions, reinstall Linux, then just when back in Linux I copy /home and /etc back where they belong.
This is just my advice, take it for what it is worth. But next time you are setting up a new operating system (like Vista, if you swing that way) remember - 'many partitions make light work' or 'partitions are your friend' or some other platitude exonerating the virtues of breaking up your hard drive.