Yeah, the money part is a bit complex. I'd assume that a number of factors will affect the price, including taxes.
There are at least 2 aspects of comfort on long rides: Position and vibration. Most road bikes can get set up in very similar positions, so aggressive bikes like the S1 come in handy if you're very flexible and want your handlebars very low. (This can still work for long rides, because that distributes more weight on your upper body and core.)
With vibration, it's unclear if a bike with more or less road shock affects performance. Some believe that a stiff bike is more efficient, others believe that vibration can cause fatigue. It also depends on your own preferences -- and whether you're talking about a metric century (100km) as opposed to an imperial (100 miles / 160km).
Unfortunately it can be hard to make a specific recommendation. I would say that if you plan to ride competitively, the S1 is probably a better option. If you prefer a little bit of comfort, plus bikes like the Roubaix are a better option. If you know which way you're leaning, that can help narrow down the options.
By the way, from what I can tell Cervelo stopped making the S1 in 2010; they may be offering last years' model.