3rd Herd: This is an excellent point regarding the drafts, like Vern I just have at 'er in my original document and only print at the end (actually, lately I haven't even been printing at all since I've been submitting electronically) and rather than sticky notes, I use bookmarks and "cut and pastes" into a seperate "possible reference" document since I do 99% of my research on-line. I use the following at work all the time but have never thought to do it for my academic stuff, I'll start now though! Keep the rest of the pointers coming as well, I wish I had them years ago when I started down this road.
How to do "drafts" electronically:
In Word you can use "Track Changes" (Tools -> Track Changes) as you work through your drafts to keep track of what you have done in order to avoid ending up with 15 different versions of the document on your HD. This will also bring up the reviewing toolbar where you can see the revision history by hitting the Reviewing Pane button. This shows the changes, lets you jump to it and stamps it with the date and time the change was made and who made it. You need to make sure that you have "Track Changes" turned on everytime you are editing your document after the first save though, otherwise it doesn't get tracked.
In Wordperfect you can use "Document Review" to a certain extent (File -> Document -> Review) but I'm not sure how well this actually tracks and retains the changes for the purposes being discussed here.
My computer with Open Office on it is gutted and all over my dining room table at the moment (making my wife VERY happy) but I'm sure it will have something.
Unfortunately after a brief test there doesn't seem to be much ability to carry this over if you change document formats between Word and Wordperfect.
WARNING: Word will be storing all of the info from the "Track Changes", not to mention personal info such as your name if you input it during the setup routine, as meta data which you can't see. Although this may not concern everyone, for some this could be a huge privacy issue, particularly if you're planning on putting your document up here. Some possible solutions and reading:
How to minimize metadata in Office documents
Office 2003/XP Add-in: Remove Hidden Data