Very good list thanks for putting the time in to write it all down.
I'm going to plug Microsoft, which you have largely steered clear of. I know it isn't cool to love M$ but they do make some fantastic software. Windows 7 should probably be your go to OS, unless you want something that it doesn't offer (Unix command line, $0 price tag)
MS Office is still by far (IMO) the best office suite there is. Word, Excel and Powerpoint are all great and if you are a student you can get them for an okay price here. Notepad++ is a great program for programming or the like if you need to manage plain text files, better then Microsoft's offerings Word/Notepad/Wordpad. If you are writing a document however, I still think Word is second to none.
MS OneNote is an amazing program it is basically a digital notebook, I don't know if there is another program like it. It is awesome and really helps me keep organised.
For document managing I use SyncToy. I regularly use 3 computers (Work Laptop, Home PC and Netbook) so I synch my documents folder on a thumb drive between all three and two backups (one external drive at work and HTPC at home) paranoid, I know. My Documents folder is ~8 GB so that eliminates DropBox and Mozy for backing up, Windows Live Skydrive doesn't let you upload and synch folders (as far as I can tell). I have been meaning to try google docs as a backup solution.
I've been using Windows Media Centre, but I just tried out XBMC and fuck, I think I'm swapping to it, thanks for the suggestion. It appears to be very fast.
Also Internet Explorer (don't stop reading) 8 and now 9 are fast catching up to Firefox, Chrome etc.
Enough of the Microsoft advertising....
Only other thing I see missing is Filezilla, for FTP management.
If you want to be cheap use the windows built in ntbackup or synctoy to back your stuff to an external device.
Trust me it's not hard.
I use Microsoft's Synctoy to back files up to my external HD. It's free and pretty simple to use.
Windows? There is a free program from Microsoft called SyncToy, which is awesome and totally easy to use.
I use it all the time.
And if you are like me and like having one copy of the files on your pc and one in Dropbox, you can use SyncToy sync both folders in one click (ok, maybe two or three clicks).
You might find SyncToy (http://www.microsoft.com/downloads/en/details.aspx?FamilyID=c26efa36-98e0-4ee9-a7c5-98d0592d8c52) handy. If you've got an external hard drive, make some folders on it that match your current 'User' folders (e.g. Music, Documents, Games etc.) Then when you've got your new mahcine running, install SyncToy and sync back. A large number of my users use SyncToy on a regular basis for normal backup of files, so it's something you can keep going even once your machine is rebuilt just so you have an external backup handy :)
A cheap and excellent suggestion would be this: put the files that are still being used on the local (laptop?) hard drive. Then use the excellent and free SyncToy to backup those files to a 1 TB hard drive in an external USB or eSATA enclosure. Then to be safe, also burn finished files to blu-ray disks, and keep those disks at a different location than the computer and external hard drive.
SyncToy- x86 if you have a 32 bit operating system
A good enclosure (most are good). I have this one, that's why I link it, but it's $54. I don't remember it being so expensive, and I'm sure there are cheaper ones that are just as good.
Blu-ray burner - $79 you'll need another external enclosure for this if you only have a laptop.
PCI File Recover is the one that I use
Look into automated backups, as well, you can go really simple and get MS Sync Toy or start looking to into working with an SVN or GIT for backup and recovery
<strong>SyncToy</strong> is a free Microsoft tool that allows you to synchronize folders. Good for mirroring files on an external hard drive.
Since I'm tight on money and wanted to go with a quick to set up and cheap but effective means of backup I have turned to some free software solutions that Microsoft offers for backup/mirroring my files. These may not be as great of a solution as others have suggested but they still work.
For local backups/duplication I use Synctoy Which is very easy to set up folder pairing that you could use to duplicate to a network, secondary or external drive.
For offsite I use Windows Live Mesh where I've set up a pairing from my local machine with a machine I have at my office and an external drive I have connected my laptop. This gives me 3 constantly updated copies of all my files. I'd highly suggest manually copying the files via an external drive if possible before setting up a pairing though as syncing RAW files can take a very long time.
Once again, these aren't the greatest or most elaborate solutions, but they're a real quick and cheap way to get some sort of backup while you figure out a more permanent solution.
Edit: Also note that I'm a just-starting-out hobbyist so I typically don't have a large number of additional files to worry about daily. If that were the case Live Mesh would likely be too slow to be useful.