Bitcoin is starting to hit scaling problems. Look at Mt. Gox Bitcoin transactions unconfirmed after 2 hours. 155 in the queue right now, but numbers from 400 to 1000 have been seen. Also look at average transaction confirmation time. During busy periods, it's been spiking up lately. There's now enough transaction volume to temporarily saturate the network. This isn't happening all the time, but it is happening frequently now.  Mt. Gox has been getting complaints about how long it takes to confirm transactions, so they've bumped up their fee to the point that theirs should get through.

Many of the mining pools are only generating 250K blocks as a default. The Bitcoin client can be configured for bigger blocks, but it doesn't have to be. There are negative incentives to miners in making their blocks bigger - their confirmations slow, and there's a risk of an orphan block.   This is slowing confirmations. A bigger fee can get your transaction confirmed sooner.  See https://bitcointalk.org/index.php?topic=339505.0