Okay, so I studied the Bikesport Michigan website and searched all the threads here on cable routing, and got some great advice - but one question remains (for bar-end shifters mounted on aero bars): Is it better to pass the right (rear) shifter cable outside of the brake cable, or loop it inside so it sits on top of the brake and can’t stick out sideways? I can’t see from any of the pics, and am undecided as to which way is cleaner.
Thanks! 
Cable routing has always been a pet peeve of mine. There are a couple of things that help determine how my cables are routed. First of all I want the most direct route from where they are originating to where they are terminating. Second, I want to use the least amount of cable as needed. Third, I want the cables to be tucked in as much as possible. The third point sometimes neccesatates over riding points one and two slightly.
On my bike, I have a Syntace base bar and C-2 clip ons with bar end shifters. For the shift cables, they are under the bar tape for the first couple of inches, and then held close to the bar using zip ties almost all the way to the base bar where they then drop down to the external cable guides on the down tube of the frame. To answer your question, mine are routed inside of the front brake cable, but they are not resting on the brake caliper at all. There is just enough extra cable there to allow for the bars to turn side to side. I have never understood why some shops route the cable up above and over the base bar. This not only adds extra cable housing, but also creates an awkward angle for the cable entering the cable guide on the frame.
i believe i queried similar questions about routing a while back and tom d. offered some good advice. i agree with mr. plumb as to the routing of the shifter cable… route it on the inside of the brake cable. if you put the shifter cable on the outside of the brake cable, you could have some problems if the handlebars are whipped to the right as the top of the caliper (or the brake cable itself) would put pressure on the shifter cable where it enters the downtube cable stop.
on another note, i actually routed my shifter cables over the base bar as (to me) this created a cleaner front end. i’ve zip tied them to the extensions, then ran them alongside the stem and head tube. on my set up, they make a gradual bend into my cable stops. i’ve found that this keeps the cables from catching anything while in transport or in the transition area, and keeps them from hitting the wind first… not that it would affect my bike times in an adverse way.
In a similar vein. Which way do you prefer your bar end shifters mounted?
as a matter of function, I don’t think it really matter which way you have them. From a psychological standpoint, I have them set up so for the rear, I am pushing down on them to go faster (like a gas pedal in a car). So as I crest the top of a hill and hit a big downhill, I just drop the shifter down.
This picture isn’t quite close enough unless you have really good eyes, but it gives you an idea, you can’t hardly see any of the cables, they are either hidden or in line with the frame.
http://www.brightroom.com/view_user_photo.asp?EVENTID=2404&ID=4506451&FROM=lost