Saddle hurt, saddle sores

a badly fitting bike can contribute to groin/buttock area discomfort.
rocking of hips due to a saddle too high or a position that curves your lower back and rolls the pelvis back will put more pressure on the sit bones.
i see plenty of hipsternodders™ with heads and hips swaying from left to right as they spin because the saddle is too high and with their arms and shoulders locked because the bars are too narrow.
(as opposed to the more common ordinary nodder who rocks in the opposite direction, backwards and forwards due to thrashing a big gear on his bromton)

decent padded shorts are the best answer but also the liner type shorts from sugoi are good as they are thinner material so can be worn under other casual shorts/jeans. i tried those dhb coolmax pant things but they are just a cheap flat pad. wore them once and found them very sweaty and never used them again. i guess they are made of cotton? which is not ideal for cycling clothing.

edit: not the dhb's in the link above these were just grey boxers with a flat unshaped pad in them them.

edit: these are the female version of the sugoi's they are made of airtex type material so you would wear something over them.
http://www.gearforgirls.co.uk/product/rc_pro_liner/