A few thoughts, little things:

• would it be possible to display the node id for a post in the grey bar with the Title, Author etc in it? This would make it easier to refer to posts by id. I know you can move your mouse over the link to find out the id, but it would be nice to have it more visible. Perhaps this could be something that you could turn on or off in your options.
• perhaps putting up a couple of screenshots of the different themes available would make it easier for people browsing their options page to check out what Perlmonks could look like?
• if you haven't set your Note depth or Note text threshold, the fields are blank on the options page. Could the defaults be filled in here?