I mix it up. Sit and spin, in the drops or on the tops (~85+ rpm); Slide back on the saddle, hands on hoods, and mash gears a bit (~66-80 rpm). Stand and hammer bigger gears (~45-55 rpm).
If i'm out of breath, I'll pedal slower; if my muscles ache, I might pedal faster. Or slower and stand, depending on which muscles hurt and why.
They all work slightly different leg muscles. None are particularly 'better'. Actually, standing is probably the worst, since it works your muscles AND your heart harder. But it engages my inner quads that don't otherwise get full extension while riding; on long rides, it's crucial to me to keep those from cramping up.