Several of the apps I use, including SuperDuper and Default Folder X didn’t work properly with El Capitan, but SuperDuper has already been updated to regain compatibility and Default Folder X has a new version on the way (and a workaround in the meantime). Most major OS X upgrades feature a lot of under-the-hood security improvements, which is a good reason to stay up to date, but some of those changes can also break software. In the case of El Capitan, a few of the apps and utilities I rely on weren’t initially compatible, but most have already been updated as a result of Apple’s summer-long testing period.