The 1.05 Patch

A patch where they decided to completly change the whole gameplay system. It changed the weapon's bullet damage so AK-47's and 92FS would be as basically be as powerful as the "Power Weapons" (M4, Desert Eagle, Grenade Launcher). AK's would now only need 5-6 hits  to anywhere on the character , even the leg , where as Pre-1.05 it would take 17 hits to the leg. Many people including myself believe Naughty Dog added this patch because of the CoD/MW players that recently got the game for Christmas (The Patch came out during February) were frustrated with the damage and felt people were not going down quick enough. Basically they just wanted another CoD game. With the damage system completely changed now, there was no need to go out to get the "Power Weapons", so you could just camp and have the Situational Awareness booster on. 

The 1.06 Patch

This basically made the FAL and the Grenade worthless. Many people complained that the FAL was too overpowered since 1.05 (I agree, it only took 1 clean burst). So what Naughty Dog did is decrease the rate of fire by 10 %, this made a significant impact on the use of the FAL, player's using them are very rare now. Now with Grenades, they decreased kill radius of grenades by 1 meter. While this might have been a good move to stop the 'Drop a Nade when you're dead tactic: it made throwing them pointless. Imagine this, someone is covering behind a wall, you throw a grenade, when they see it coming they can just roll right away and shoot you as it won't affect them.

This person knows exactly what I'm saying as well as others just Youtube search Uncharted 2 1.05 or 1.06 – http://www.youtube.com/watch?v=CeO9rvUS94s

1.07 & 1.08

The 1.07 and the 1.08 Patch didn't change much, just a few glitches here and there.

I hope Uncharted 3 will have the multiplayer similar to the 1.04 Patch.