I've been struggling with this for the past couple of weeks as well.
One of the big issues I rand into was the way different browsers
handle scrolling the results window, and how the window controls is
treated as a loss of focus in some browsers.
I implemented the code Craig posted in this thread from 2/2009:
http://groups.google.com/group/prototype-scriptaculous/browse_thread/thread/ee29de995b4e000d
... but that introduced some other aberrant behavior, such as the
results box not going away after selection.
Would love to see how other people have solved some of these issues.