So on my MacBook Pro, I ended up giving up on Fink after a little usage (Fink Commander was having another hissy fit when I last used it). Anyhow, I decided to use DarwinPorts instead, because at the time I needed a copy of cracklib installed somewhere for a class project. It worked out pretty well, and has since continued to grow nicer. They have renamed the project to MacPorts and are hosted by Apple (afaik).
Today I went to upgrade all of my ports since I was using my lab desktop and my laptop was sitting mostly idle, only to discover I had multiple copies of many of my installed ports. When I tried to uninstall them it refused, noting that they were depended upon. This however was not true though, since they were inactive and a newer version was being used. After a little googling and a look at the man page, I found out the following command would do the upgrade, and forcibly remove the currently installed version
port -fun upgrade outdated
After using that, I forcibly uninstalled all the inactive ports I had (since if something really bad does happen I can always downgrade them, and these are more toy apps, not mission-critical). Now I have a single copy of all my ports installed, at the latest version; this is very good since I’m already running out of hard drive space on my laptop ’cause I haven’t learned to temper my free iTunes downloading of video :O