Having apps owned by root is not a problem, unless they have the suid bit set (you cannot set this bit from the GUI; it has to be done from the CLI). No app should run suid, and especially not suid root, unless it is absolutely necessary. Only one app needs this on a standard OSX install: Classic. X11 needs it too, but that's not a standard part of the install.
However, having apps owned by root is not a problem in and of itself. Most of your CLI programs already are, in fact.