The one chord drilled into my unconscious mind is:
E:0
B:0
G:3
D:4
A:4
E:2

just because I've heard Vai use it so much live. I'm a big fan of creating these 'cluster' chords everyone has been talking about lately. Two others I like are:
E:12
B:10
G:11
D:0
A:x
E:x

E:0
B:0
G:8
D:6
A:4
E:x