Originally Posted by nathand

Are the holes consistently in the same location on the tube? I got several flats on one wheel, no obvious cause to me - I'd just find the tire flat when I went to ride the bike. The hole was always near the valve, on the side of the tube facing the rim. When I went to my LBS to buy yet another tube, I mentioned the problem to the mechanic. He asked some questions about the bike (I hadn't ridden it there, due to the flat tire) and he noted that that particular bike had come with narrow rims. I'd had trouble seating the tire bead right near the valve due to this. He suggested that I was pushing the valve up, into the tire, so the bead would seat, and that this allowed the tube to fold over on itself (making sort of an S shape next to the valve). Then, once inflated, the sharp bend stretched the tube until it failed. Now I use the valve stem nut (Presta valve) to lock the valve against the rim, and I haven't had another flat.

You might not have the same issue, but mechanics have a lot of knowledge - might be worth bringing your wheel to your local shop and asking for some help, if you can't identify the cause.