Also, there are a lot of subtle things that won't work if you are logged in as a superuser (the default "host" account is one).  For example, any module that uses the "user" table for configuration won't work because the superusers are stored in a different table, you won't be able to add the superuser to any groups because according to the system they don't exist.  I started out with my main account as a superuser, but ended up running into so many little problems here and there that I created a new account that was only an administrator, and kept the superuser account only for host-level functions.  Things run much-much smoother that way.

It worked for the majority of the core modules, so that wasn't an issue.  However, third-party programs aren't always so forgiving, and a couple of them I tried made it almost impossible to use a SuperUser account with.