As a web designer, I suppose I must give this thing a nice constructive criticsm...
Hmm lets, see, the background looks fine, but the navigation bar seems lost in all the layout, dont use grey for the buttons, I'd use black to make them visible enough.
Also, all the gradients looks nice, too web 2.0 for me, but that's just my own opinion.
About the header...hmmm, I know you need that space for ads...but, that image (the PCSX2 one) looks... dont know, its like 3D and 2D does not mix. To tell you the truth, it looks awful to me. A nice 2D text without perspective would look perfect here, also, if the header is giant like that one, you'll not see things like the navigation bar or other important info.
I'm not an "official" web designer, but I was a webmaster of a site for a few years, and that also involved doing my own design for the site's forums (keep in mind I have no real training or professional ability in the field, and my work was, in my opinion, okay and better than average, but nothing super exceptional), but I agree overall with this, except for the last part.
I'm not sure what all the hate about the logo is for. It looks excellent to me, but to each their own. I do agree that it's a bit too big and needs to made smaller for the reason stated, but the logo itself, to me, is fine.
Otherwise, the buttons and navigation bar do need to be rethought as well (again, the quoted text's examples would be perfect solutions), but otherwise, I like the new direction, and that says alot considering I expected to come in liking the old format better (since it was pretty good too).
I like the gradients, and the old layout seemed 2.0-ish to me as well (which looks good if it's not done just to look that way for the sake of it, and i don't get that feeling about that design).
Overall, good job. It's not perfect, but if you make these changes, someone else will have tips to make it better at something from that point, and so on no matter what design you settle on. A solid 8.5/10 from me (9/10 with some changes made).
Also, you you just need to make the forums match. The layout they have is too different from the main one, and in my opinion, doesn't look so great anyway.
P.S. I hate to ask this here, but I registered at the PCSX2.net forums a while ago, and never got my confirmation e-mail. I'm pretty sure I typed my e-mail in correctly, and it never ended up in my spam folder, so could someone look into that if possible?