I got the YLOD about a month ago, so I did the reflow method, and I noticed that while it was running there wasn't as much heat coming from the side of my Playstation. Then, about an hour later, it yellow lighted again. So, I reflowed again, and it was working for about an hour, and yellow lighted again. This is my third time reflowing, and I have the case off while it is running to make sure the fan is running and everything. I tried it for about five minutes to make sure everything is working right, and it pretty much is, but it just seems like it isn't dispelling as much heat out of the side as it should. The fan is running, I put Arctic Silver on the GPU and CPU, I don't see why the heat isn't being blown away from the console. After a few minutes of running, the residual heat made the PSU so hot it felt like a stove eye. Someone, please help. What is going wrong? If I try to use my Playstation before I get this fixed, I know it will just yellow light again.

In general, it isn't good to have the case off of anything that has specific airflow. Although I don't know much about the PS3's internals, if the fan/s in there push air a specific direction, you don't want to have the case off for the most part as the fans lose their effectiveness (air gets redirected up and out instead of over the components and out the vents). Some components in all computers get really hot regardless, usually those components are graphics cards, but PSU's can get fairly hot as well. Unless you smell burning, high temperatures aren't usually a problem as lots of stuff is built for operation at high temperatures. (Everything I said is stuff from the PC side of things, they might not apply directly to the PS3).
 
That being said, any reason why you went the DIY method instead of calling up Sony? 
 
Hope someone else can be of more help.

" @commandercup:  Well, with the case on, it got hot enough to yellow light again. And the way the vent is designed on the side where most of the air comes out, it would still be pushed in the correct direction. It just isn't being pushed in the right direction it seems, with the case on or off. "

" @commandercup:  Yeah... That's what I was thinking, but I figured I'd wait and see if there was maybe another fix before I tried that since the fan is still spinning up. I guess I'll try that. "

 Does anybody know if this PSU is defective or if they all get too hot to touch like that on the older fat models? 

You may still be able to send it in to Sony. I heave heard a lot of people who have opened there ps3 sending it in and still getting it fixed, so long as there are no obvious signs you damaged it.
 
After you get the YLOD can you still turn the ps3 on after it cools down? Because reflowing as i understand it is to resolder a bad connection. And if you can still turn it on then you can at least narrow it down to just a overheating problem and not a bad connection.

Never mind... I tried to update and my PS3 turned off during installation. It's at the landfill right about now.