Additional internal storage – very important if you want one and only one Mac.
Double the RAM ceiling - 8 GB on the MBP versus 4 on the Air. And the MBP is user-upgradable, which feels better to me.
You also get longer battery life with the Pro, but since I'm not usually that far from an outlet, it's not a big deal. I'm also happier to have an incrementally faster and later-generation processor, since that'll hopefully grant a further 6 to 18 months usable lifespan for the machine.
http://paulstamatiou.com/ssd-raid-performance-9-months-later
I'm waiting until Lion comes out for any more hardware changes. Now that I'm using Jekyll locally (and will be just rsyncing the files) and it needs to regenerate 1000+ posts with layout etc changes, the core 2 duo is showing its age. And I have LSI disabled..
Macbook Pro 15: $1800 + $250 for 128GB SSD
Macbook Air 13: $1300 + $100 for 4GB RAM
Both machines will have the same size SSD, RAM, and same number of pixels, but the MBP will be $650 more.
(I know there are other ways of configuring the two, like adding a $100 hi-res option to the MBP, or adding the $100 MCE OptiBay like you did. I ignored them for simplicity and to create a more apples-to-apples comparison.)