The application situation
A fairly large component of making the switch to Linux is finding equivalent applications for your workload. If you've already been using open-source applications for most of your work, the hard part is already over: Chances are you'll be able to use the exact same applications in Linux as you were in Windows.
For instance, if you've already been using OpenOffice.org for word processing on Windows, OO.o documents will open as is in the Linux version of the program.
However, if you've been using Windows applications exclusively, then you'll need to locate equivalent programs -- apps that accomplish the same tasks or work with the same file types.
One place to start researching where to find equivalents is a regularly updated page on the Linuxsp.ru site, which breaks down applications by category, listing Windows and Linux equivalents in parallel columns. The breakdown also goes by subcategories of product -- e.g., "Email client in the MS Outlook style" is one useful subcategory. The site also has some discussion of feature equivalencies between Windows and Linux as well.
If you have files in a given format and you're not sure if the replacement program you have in mind will accommodate them properly (and you need to be sure it will), you can try this experiment before committing to anything: Get your hands on a live CD distribution of Linux that contains the equivalent program you're considering as a replacement. Make a copy of the file in question, put it on a separate drive (such as a removable USB drive), boot the live CD, and see what you can accomplish with the file.
For instance, if you're planning to replace Photoshop with Gimp, you may want to find out if the images you want to work with can be opened or edited with Gimp in the way you want. It's important that you attempt to do this in Linux itself, so that you'll know if the current Linux edition of the program can accomplish what you need; feature sets can vary slightly for a given program on different platforms.
My advice to handling documents during the migration process is that you maintain at least three copies of any given document:
1. The original file, as it was before you started the migration process. If you're preserving your original Windows partition, the original file could be kept there as part of that.
2. An offline backup of No. 1; that is, a copy on another drive or medium for safekeeping, possibly the drive you used to perform the migration.
3. The migrated copy, which you're working with now, which may have been converted into a new document format.
If you're migrating away from proprietary file types -- for instance, from the "classic" Microsoft Word format (Word 97-2003) to OpenOffice.org's OpenDoc -- it's best to take the document in question onto the new platform, save it in the new format before attempting to do any work with it, and compare it against the original to see if it has survived the conversion process.
Most Word documents translate as is without trouble, but keep an eye on documents with exceptionally complex formatting. (Math formulas in Word documents in particular have been known to cause problems for some users.)