Were you looking for the road forum? Still, not a bad question for this section but I suspect most of the posters here ride older bikes than yours.
IMO, there have been two major "improvements" since your bike: threadless headsets and external bearing cranksets. The crank would be a straightforward swap but to upgrade to threadless you'd need a new fork, headset, and stem. Combine this with a new wheelset and I think you could have a bike almost as light, stiff, etc as a new bike.
However, this would add up quickly and you'd still be left with a 16 year old carbon frame. If you're looking to upgrade it would probably make more sense to sell this bike (~$500) and get yourself the new Madone.