John Petrucci recorded Images and Words with a basswood Ibanez w/ a Tone Zone and Humbucker From Hell. Pull Me Under is a good example.
The Tone Zone is a great match for basswood, but can be a bit loose and has rolled back treble. Sounds especially good boosted IMO. The D-Sonic is another good choice, it's tighter and a bit brighter with just a bit more output.
Here's my favorite clip of the D-Sonic/Air Norton combo (though its in a poplar guitar, but the basic sound is the same)