The single most important thing you can do when creating a custom CMS is make sure it is easy to add additional features to it.
We had our own CMS programmed about 2 years ago and we were happy that we made sure we could add additional features to it as we needed them.
Our app went from just being able to handle images, movies, stories, games, plugins, and upsells for a paysite to a fully functional, automated free site and avs site builder in the space of about 2 months.
We're also working on some additional features that we want the guy who coded the script to add over the next couple of months including click tracking inside the members areas to see which types of content are getting the most interest from our members through to a simple random 'feature of the day' setting.
Also, be sure that you can create custom templates for each site you utilize the CMS on, this has been a lifesaver for us when it came to figuring out which members area layouts worked the best for specific niches
Regards,
Lee