If long rides leave you full of aches and pains, it's possible that your bike isn't adjusted properly. A bike fit will help you (or your local bike shop) make the appropriate adjustments to help you ride efficiently and in comfort.
BikeFitting.com - available through Merlin and Litespeed dealers.
Fit Kit - popular system available through many bike shops.
Serotta Size Cycle - utilizes a fully adjustable stationary bicycle to determine your ideal fit.
WobbleNaught - uses laser measurements, EMG (electromyography), and force plates to develop a scientifically precise fit.
Bill Boston Cycles markets Accufit software and offers several articles on bicycle fitting.
The books referenced below contain chapters on bike fit: