I have only had my 2004 5900 for a few weeks now but have put a few hundred miles on it, even with all the wind & rain here in Devon. All I can say is that the frame really makes the ride a smooth one. The 110 carbon soaks up all the bumps & is so light & stiff that it makes hills a breeze. It's an absolute joy to ride.
Let's face it, the Madone & the 5900 are both pretty bikes. Both are pretty pricey too but if you're shelling out your hard earnd cash get something you want. I can only suggest that you take out a Madone & ride it. If you fall in love with it great, if not try another manufacturer. I doubt you'll find a bad bike out there for the money your looking at spending but it's all about personal preferance. Some will love the Treks others Giants etc. Then there's the whole issue of whether you want carbon or titanium etc.
Some will say if you crash the carbon is history, well, true, but the same can be said for many other materials. I doubt anyone would want to crash their £3000-£5000 bike! If the Lance crash in the '03 tour puts you off the Madone (although it was an '04 5900 he crashed) maybe titanium is better for you? Some carbon bike, such as the Orca, have rear triangles that can be removed so a crash like Lance's won't mean the end of the whole frame.
Okay, I'm going on a bit but I'm sure other Trek OCLV riders will tell you that it's all in the ride - Take one out & try it. Please let us know what you end up doing. Either way, if you're spending this sort of money you're going to have a fantastic bike beit Trek, Giant, Colnago, C'dale, DeRosa etc....the list goes on...
Pez have a few articles on the 5900, Orca & a few other carbon bikes, check it out:
http://www.pezcyclingnews.com/?pg=technspec