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.
Considering how often Data successfully took over, it makes "Redemption II" even more daft with the hokey drama and passive aggressive nonsense coming out of them:
RIKER: Starfleet is stretched pretty thin across the quadrant. There are only about twelve ships within a day's travel of this position.
LAFORGE: The only other ships available are either in spacedock for repairs or still under construction. Most of them don't even have full crews yet.
RIKER: We could probably scare up seven, maybe eight, more ships.
PICARD: Mister La Forge, can you implement your tachyon detection grid with twenty ships?
LAFORGE: It's possible, but the more ships, the bigger the net we can throw.
PICARD: All right. I want to add the Tian Nan Men, the Sutherland and the Hermes, whether the yard superintendent says they're ready or not. Mister Data, will you select a group of experienced Enterprise officers to augment the crews of those ships.
DATA: Aye, sir.
PICARD: Will, I want you to command the Excalibur. Her crew was reassigned when she put in for repairs. Geordi, you will be his First Officer.
LAFORGE: Aye, sir.
PICARD: I want the fleet underway by oh nine hundred tomorrow. Thank you, gentlemen.
(Riker and La Forge leave)
DATA: May I ask a question, sir, of a personal nature?
PICARD: Yes.
DATA: I am confused. Why have I not been assigned to command a ship in the fleet, sir?
PICARD: Well, I felt that you would be needed here. Why do you ask?
DATA: You have commented on the lack of senior officers available for this mission. I believe my twenty-six years of Starfleet service qualifies me for such a post. However, if you do not believe the time has arrived for an android to command a starship, perhaps I should address myself to improving my--
PICARD: Commander. I believe the starship Sutherland will need a captain. I can think of no one better suited to the task than you.
DATA: Thank you, sir.
Why Picard doesn't even explain the need for Data to remain on the Enterprise, for which a justifiable reason might be there, and of which might be considerable, we may never know. As he's having to move Riker and Geordi to another ship so having someone like Data remaining isn't exactly a bad thing, what with Enterprise being the flagship and all. Plus, Data could figure out the workaround from any ship. Plus, based on those exciting moments on the Sutherland, there could have been Robson versus Sheldon Cooper bickering over procedures, rules, duties and so on, their melodrama there would be just as hokey. Maybe less hokey as I couldn't begin to buy into Data's emotionally-driven responses that he would never be used or heard of again, not even in front of Worf when taking command in season 7. Even then, when we saw the same trope used in "The Arsenal of Freedom" only this time it's Geordi vs the Chief Engineer*, that one had more dramatic and story weight behind it.Also, in a dedicated region of space, to get everyone over to it from their usual postings from the other side of the Federation territory would take lots of time, sure. But the Romulans could easily putter their fleet of big spaceships around the net because, with 12 or 20 ships and how far they can fling their field, it's just not large enough to be a detriment. Just go around it. Simple. Also, Sela too seemed to know about the adventures of Captain Data - so who told her about "the one with the android captain", but this isn't a 3-parter where Robson quietly gave the info to Sela as for yet another exciting 40-minute subplot just waiting to be told?
* It's amazing how readily interchangeable these roles are, even though both cover completely different mindsets, philosophies, relative knowledge, disciplines, etc