Its possible to back up most of the partitions manually with root and restore them if the phone will still boot but you have to be extremely careful how you go about it.
+1 re. this ^^^.
The main three features that custom recovery give you are:
1) A quiesced system that ensures that the partitions you want to backup are not currently being modified; this is done by booting the phone into a limited kernel that basically gives you just enough capabilities to perform the functions you need in a custom recovery
2) A more user-friendly menu system for invoking commands that no ones wants to remember how to type (or you'd want to get wrong when typing them
3) The ability to communicate with the adb daemon to provide the functionality that you'd want in a custom recovery
You could safely backup your /system and /boot partitions as the Bionic currently stands, but couldn't really safely backup your /cache or /data partitions since you can't ensure that they don't contain open files or files that aren't currently being modified. Additionally, I don't think you'd be able to safely restore your /system partition while Android is up and running.
Making a backup of /system would be helpful for finding and possibly restoring any individual files that one might have deleted, but your best bet would be to avoid deleting or renaming any critical system files to begin with.