I've only been driving my '05 manual a couple of weeks, and I certainly don't have any track times to share, but I can tell you I'm convinced that in a side-by-side, manual-versus-automatic comparison of two otherwise identical, right-out-of-the-box '05 GTOs, the automatic would have the edge for most drivers.
Pontiac's own literature on the GTO shows an advantage of one-tenth of a second for the auto in 0-60 times, and that edge holds through the quarter-mile. I'm assuming those times are from an expert test driver, so we can generally presume that none of us could do any better in coaxing our manual-equipped GTOs to faster times.
The automotive press has given the automatic GTO a little flak for having an old-fashioned four-speed transmission, but the auto GTO doesn't appear to care that it's being criticized: It blasts to 60 faster that just about any German or Japanese seven-speed, paddle-shifted auto-manual out there.
I got a manual simply because I like the additional involvement it affords. That being said, it's taken me a few days to be as proficient with this six-speed as I'd like, and I still have more learning to do. I had a six-speed '01 Corvette before the GTO, and a six-speed '94 Z28 before that. I think the criticism some auto writers have leveled at this manual is generally fair. It really is a bit notchy, and notchiness is the enemy of smoothness, which is essential in keeping up a head of steam while accelerating. But it's not beyond mastery, and every day that passes I feel like I'm making more seamless shifts.
I've grown to really like this transmission. It's genuinely fun. And I've gotta tell ya--leaving the palm of your hand on the shifter while driving provides a "magic fingers" pulsation that's so spine-tingling, it almost feels lascivious! That alone would convince me to choose the manual over the auto.