If you can wait another year it could be worth your while if you're looking to keep the car that long. The new iQ will be out by then and most believe the 2010 Yaris due out the end of this year will come with their new 1.33 litre power plant which is more fuel efficient. Maybe even stop and start technology.
People can always argue to wait based on getting what is new, but there are major changes coming down the pipeline this year and those are only 2 examples which could greatly reduce your total cost of ownership in significant fuel savings over 10-13 years. I won't even dare mention the Honda Insight II on this board.
If you have to buy now I'd go with the Yaris as well, for personal preference reasons and also because when you keep something for a long time having the more popular product can come in handy when replacement parts and maintenance are in order.