The only real problem I see with the stuff you have absolute control over is the transparency of the tree menu background -- having the header "eye" image and the thin rule running through the box looks a little bit weird and unfinished. At a closer look, I'd like to see a more consistent look to all of the nav boxes on the left -- the vignette effect kind of gets lost altogether by the time you get to the Premium Members box because of the gradient underlaying. Perhaps an opaque background (with a centre cutting the difference between the black of the tree box and the darker blue of the Download box) might work better. And I'd hyphenate "non-pirate".
The rest is the Google ad integration, particularly the YouTube box when it shows -- the link text doesn't contrast enough with the background. I realise that you only get so many options with the ads, but there's got to be something that's a better fit than a transparent background with blue links over a blue site background.
