Just a quick note to record how upgrading from Wordpress 2.x and Webcomic 2.x went for me. I waited quite a while until most people stopped complaining about upgrade problems before trying it.
First, I saved posts with the export tool (which doesn't give that much peace of mind because it doesn't include images). Then I did a full backup of the whole site and a dump of the mysql database. I do that regularly with a small script so that was easy.
After backing up everything I upgraded Wordpress. It had been asking for it for quite a while now, with a huge 'Upgrade to wordpress 3' button always visible in the Admin console. Instead of clicking that, I decided to go through Dreamhost's panel because there are some things that need to be setup at Apache level that I know people at Dreamhost had taken care of, so it seemed the safe bet. I also figured I could get some support if I went that way (which I didn't need btw).
The upgrade to Wordpress 3 went flawlessly. Well, flawlessly meaning in this case breaking most everything and rendering the site apparently ok but horribly broken inside. First, all comics had disappeared, which is a bit scary when your site is supposed to be mostly about that. But that was expected because neither Webcomic nor Inkblot (the theme) were upgraded yet. I upgraded Webcomic directly from the plugin directory and downloaded the latest Inkblot theme from their site. I extracted the inkblot theme into the themes directory and copied inkblot-child outside of it so that it sits directly under 'themes', I then made sure inkblot-child was selected as the current theme.
Then, I went to Webcomic/Tools and upgraded the posts. This essentially recovers all the comic posts by migrating them to the new format. It was a relief to see them reappear, as every comic post had been lost until this step. The process is easy and consists on a small wizard-like dialog with a few steps, and one of them implies you manually moving your comic files to another directory. After that, a few of the posts weren't correctly bound to their comic images so I just bound them again.
All the tweaking on my inkblot-child theme was lost, which was not a real problem as I prefer the new structure. I just uploaded a banner for the header, tweaked font size and type and played a bit with the list format.
I tested the design that I commented sometime ago, with a blueish/magenta background, but it seems to clash with white images. I'll try it again at some point.
So, in summary: