Saddle - make sure you have one with cut outs if it's your bits that are suffering, There are plenty to choose from. You might need to try a few before you settle on the one that suits you. (I'm up to 4 tried and tested and discarded so far)
Position is crucial. Make sure that the height and reach is good so that you aren't shifting in your seat as you pedal. And that the saddle is horizontal. You need it to be as level as possible.
Vaseline / body butter up beforehand. Prevent the chaffing before you start.
Good fitting shorts - I cycled yesterday with new tri shorts with no 'cushioning' and was fine in the chaffing department. Compare that to last weekend wearing my winter bike tights which are well padded but are now too big for me - oooh raw and hurty just because they were shifting underneath me. I was sudocreming big time afterwards.
But as others have said HTFU. That doesn't mean calluses. It means getting your body used to being on the bike for longer periods which you can only do by going out for longer.
Edited: 13/10/2008 at 16:54