- registry is not portable (hard to clone configs to multiple computers)
- all eggs in one basket
- accessing/modifying registry from shell scripts is *not* fun
- it's easy to mess up *anything* when making a mistake with registry (with rc files you only mess up the one particular app/function)
- if you mess up settings of an app (or want to return the "factory settings"), just delete the rc file and start over - nothing else is affected
- with registry, you often cannot be sure whether stuff there is obsolete or not
- with rc files, you can move apps to different locations without messing up the configs
- with rc files, you can reinstall the whole operating system without losing user specific configs (taken /home is mounted as a separate filesystem)