They have different cases. The 2009 one opens from the front, and the individual blu ray s are contained inside the box. The 2010 set is simply the 3 blu rays contained in a slimmer slipcase. Other than packaging, the content is the same on both releases.
Well, that one is a Region 2 release, which means that if you don't live in Europe (excluding Russia, Ukraine, and Belarus), the Middle East, Egypt, Japan, South Africa, Swaziland [and no, that's not a typo of Switzerland], Lesotho, Greenland, or certain French territories outside of Europe, you can't play it on your blu ray player unless it's a region free player. Blame piracy.
@Lawdog1881 It's common that when a new version of something gets released, the out of print one becomes rare and the price is jacked up for collectors. Especially when the old one is thought of as superior to the new edition, as is the case (get it? Case!) with the Bourne Trilogy.
(I'm copying this from another discussion. However, this does not take into account the BluRay version.) The original boxed-set release ("The Jason Bourne Collection") basically includes the three movies in their original individual packaging, now placed in a larger box. The main attraction with that version would be the 4th disc (unique to this set), which appears in a large slip-cover designed to look like Jason Bourne's US passport. It includes a series of short videos focused on author Robert Ludlum. But the "Collection" does not come cheap, currently priced at a whopping $99.00!
That probably makes the newer, slimmer boxed set ("The Bourne Trilogy") a better deal. It has an attractive, more uniform presentation. Yes, the 4th disc on Robert Ludlum is missing; however, all of the other bonus features for each film are still in place. More importantly, the newer set now includes a commentary track for The Bourne Identity from director Doug Liman--something that was missing from the earlier release. Since director commentary is now available for all three films, this is the set worth having. And with Amazon's discount (it's currently priced under $20.00), the choice becomes obvious.