I always go for the manual transmission. My current and long-term ride for the future is an 08 Jeep Wrangler Unlimited Rubicon with a 6-speed manual. Last spring, I sold a Pontiac Solstice that had a 5 speed manual.
My previous vehicles were all manual transmissions, with the exception of a '99 Silverado and an '03 Tahoe.
FYI--While she prefers an automatic, my wife drives a manual transmission better than most guys I know.