When prepping for the IBR I cut out caffeine and exercised regularly. Ditching caffeine was very helpful on rides lasting longer than 12 hours. Learning to hydrate properly also made an enormous difference in my stamina (forcing myself to keep drink water/Propel, and even Boost on long rides was also a major breakthrough).
I also had an athletic trainer design a workout for me. It was pretty intense and focused on core muscles, legs, and general conditioning. I barfed the first time I did it.
(I was actually sick from the flu at the time, but didn't want to stand him up. Bad idea).
Some of what I did at the gym looked a lot like the workout shown in this video.....http://www.youtube.com/watch?v=SsYLBO25nKY
No matter what conditioning you do, there is no substitute for riding. Building up days from 200-1000 miles, and riding multiple days of 300-900 miles in a row made all the difference for me in getting things like foot position and seat right, and for setting up the best plans for my tank bag/side cases etc.
Of course that was 18 months ago. Since the IBR I haven't done a day longer than 500 miles (and that was on the way back from the IBR!) I'm a sorry sack of s**t now and I bet I'd be sore after a 200 mile ride.
I gotta start planning longer rides again.