Which is more painful, carpal tunnel syndrome or ganglioncyst?

Depends: Both can be bothersome. Cyst symptoms are typically dependent on the location of the cyst. They can be painless but can also be aggravated by activities. Similarly, carpal tunnel syndrome can be mild, moderate or severe. In my experience, carpal tunnel syndrome is more bothersome to patients.

Both can be painful: A symptomatic ganglion cyst can generate dorsal wrist pain, especially with certain positions causing terminal wrist flexion or extension, or with heavy lift or grip. Severe or long standing carpal tunnel syndrome can also result in hand pain; in addition to hand numbness/tingling, and decreased dexerity ("dropping objects"). Further medical evaluation is recommended for persistent pain.

Both: Both can hurt. Ganglion causes localized pain. Pain, numbness, tingling, weakness and night pain are the most common symptoms of carpal tunnel syndrome.