I prefer root explorer because of the one-button switching of mounting from R/O to R/W and back again.
I prefer Root Explorer as well because it is one of the few file browsers I have found that will allow you to edit files under the phone's "system" directory. For instance I use root explorer to edit my keyboard button mappings or to copy ringtones or alarms into the phone's audio directory. I believe File Expert will allow you to browse the system directory but does not give you the ability to edit text files and such.