From the top of my head, times where Data was in command of the ship, temporarily (meaning both Picard and Riker were off the ship or incapacitated) or otherwise...
"Justice"
"Angel One"
"The Vengeance Factor" (implied, since Picard and Riker were both on the Gatherers' ship when Riker beamed over to stop Yuta)
"The Hunted"
"The High Ground" (implied, since Riker was leading the away team to rescue Picard and Crusher)
"Clues"
"Night Terrors"
"The Mind's Eye" (implied, since Picard and Riker beamed down to talk to the governor)
"Redemption II"
"Tapestry" (implied, since Picard and Riker were on that away team in the very beginning of the episode)
"Gambit, Part I"
"Gambit, Part II"
There are, of course, many times where he was in command of the night watch or when Picard and Riker are off duty or otherwise engaged with things aboard the ship.