OK, here are the things that can help:

Brooks Saddle: A Team Professional is probably the best to use on a road bike. It is absolutely the most comfortable saddle availible in it's size.

Cross-laced spokes: Radial and semi-radial wheels transmit a lot of impact. a set of wheels 3x front, 3x or 4x rear is not only comfortable, but stronger, too.

Tubular Tyres: Yeah, they can be a royal pain in the @$$ to fix, and they are more expensive, but they do ride better.

Lower tyre pressure: You don't need to inflate them to maximum pressure. Tubulars can even be run at very low pressures (sometimes I will run my front as low as 70 psig) without risking pinch-flatting.