Paste and Match Style
Sometimes you've got some text on the clipboard, and you want to paste it in to your page. But you know that since you copied it from Safari or Word that the text styling is just not going to match what you've set up on your page. And what a bummer that is. But wait- we've got that problem solved! Under the Edit menu, right next to the Paste command is another command labeled "Paste and Match Style". This will take what's on the clipboard and paste it into your page without any funky formatting. Just nice clean text the way you like it.
Custom URLs
Did you know you can have a word or phrase link directly to a URL, so when clicked on it will open up in Safari? Choose the Edit->New URL... menu item, and enter the address (such as "http://flyingmeat.com/") and then the phrase you want to link to (like "Flying Meat" or something). Now whenever you type "Flying Meat" (or whatever) it will highlight and open up in your browser when clicked on.
To delete a custom URL, bring up the document info panel, and delete it from the table named "Files and URLs".
Following Links with the Keyboard
If the insertion point happens to be on a link in VoodooPad and you want to open it, you don't have to reach for the mouse. Just type command-L and VoodooPad will do the right thing. Instead of creating a new page it'll just open up the link that you are on. It even works for multi-word links so you don't need to worry about selecting it first.
VoodooPad & LaunchBar:
You can directly open a page by name with launchbar (in 10.4). Find out more from http://flyingmeat.com/board/viewtopic.php?t=205
Quicksilver, too
The Launchbar tip works in Quicksilver. Just add the same folder to the index.
Including the output of scripts in from your clippings folder.
If you create a unix shell script, and place it in VoodooPad's clippings folder, it will be run when selected from the insert menu, and then the output created from the script will be inserted where you have the cursor.
Setting $PATH or other variables for scripts run from VoodooPad
If you want to set environment variables for your shell scripts, have a look at this Technical Q&A from apple:
http://developer.apple.com/qa/qa2001/qa1067.html