It's been a while since I've said anything about VoodooPad here, but it deserves another round of kudos - I continue to absolutely live in it, and it gets much more useful the longer I use it.
How I use VoodooPad
I keep a running set of time-stamped pages under "ResearchLog" and "MeetingNotes", and all kinds of linked notes from there that I constantly search, occasionally refactor and refine. "MeetingNotes2006-03-21" leads to "ResearchLog2006-03-22" and so on. With a simple python script to automate making new "Notes" pages, I don't have to work too hard to keep the organization and index pages going, and it's proved to be really useful to recall what I did when, and what problems I ran into.
As I work, I keep a running log of what I'm doing in each ResearchLog page. What I've found most valuable is that I copy in verbatim command lines for configuring and building software I'm using for research (including my own) so I can recreate the same environment elsewhere. This kind of thing has saved my sanity over and over again, enough that I can't imagine working 'bare' (without a VoodooPad window open next to my terminal) any more than I can imagine working without Emacs.
A tip on style
A little attention to text style makes my notes pages more useful and easier to find in the Expose soup. I started using a larger font for the top header and description of each page, so I could distinguish pages easier, and it's made everything a little more pleasant.
Here's a typical set of VoodooPad windows for me - a jumble!
This zoom shows what it looks like at 100% - the large-print title helps me find the window I want without the Expose "scrubbing":
Still, I don't want to have to keep doing this all the time, so I made use of the "NewPageTemplate" page (documentation) and set the styles there - now all my new pages have the style I want, and I don't have to keep using Cmd-Opt-c and Cmd-Opt-v (copy and paste style) over and over.
Update: One comment asked for larger images, but since you probably don't want to see my research notes anyway, here's an RTF file with the contents of my "NewPageTemplate" page.