Just the other day I went to the bike room after work to take the bike for a short spin before spending the evening dowtown. The rear tire was flat (a 25mm Vittoria Zaffiro). I pulled the tube, located the hole, then checked the corresponding area on the tire. Nothing. I figured, "well, must have run over something that did not stick in the tire." So I replaced the tube and went for a 40-minute ride around Stanley Park. Returned to the bike room, dressed and went out for the evening. Returned to the bike room about four hours later. Rear tire flat again. Pulled the tube, same size hole (pin-prick), exact same location. Re-checked the tire. Nothing. Could feel nothing sharp inside the tire. No holes near the bead where it might have worn. Total mystery. Inserted a new tube, but this time pumped it to only 100 lbs instead of the usual 120. Made it home. Tire still holding. Next morning, still holding. Switched wheels, then pumped the offending tire to 120 lbs and left it. Still holding air. Replaced the tire anyway with a Vredestein DuoComp 25mm (the TriComp is not available in 25mm). We'll see what happens. The hole is on the tire side of the tube, so I don't think it's a base tape/rim issue.
Total mystery!