For open chords, I tend to keep my thumb up over the top.
For E-string rooted chords, this tends to mean I'm gripping the neck with the heel (rather than tip) of the thumb.
For A-string rooted chords, I tend to use the thumb to mute the E-string, allowing me to strum all the strings (where I'm not playing a base note first rhythm). The tutorial for (I Can't Get No) Satisfaction (Made Easy) has an example of this.
-Iain