If you're looking for comfort, then the Roubaix wins handsdown, no contest really. Everyone that has a Roubaix loves it, saying how its the most comfortable bike they've ever owned. HOWEVER, the Madone is much more popular, simply because most people that shell out that kind of cash want a race bike with a racing geometry. The Madone is somewhere in the middle between a Specialized Roubaix and their Tarmac in terms of comfort vs. aggressiveness. If you go with the Madone, I would ditch the Bont wheelset and get something more durable.
If you're going to do more long distance, I would go for the Roubaix. If you're interested in racing at all, then I'd go for the Madone. Both are awesome bikes, so test ride both (with a good fitting) and it'll be pretty clear which one belongs to you.