My best guess is that transactions of very low amounts (and especially very low fees) are the ones with looooong confirmation times. 

Two examples:

1)  A few days ago bitmixer sent a small payment to ME, but it took some 40 + hours to confirm (as they sent the payment with a close to $0.00 miner's fee).  I did get it confirmed, but it took a long time.

2)  As a test during perhaps the worst of the "stress test" / spamming / attack (July 6), I sent myself a small transaction of about BTC0.005, but with a large fee: BTC0.0006 ($0.16).  The transaction was confirmed on the next block.  Reconfirmed on the one after that.