Incredibly slow performance on early 2011 17-inch; what could it be?

Question

I've got an early 2011 Macbook Pro 17-inch with the (at the time) bumped up 2.3 ghz CPU. Other than the CPU bump, it's pretty stock. Only 4 gigs of RAM, and the 750 gig hard drive running at 5400rpm. This is my second unit, the first having mysteriously died when I was traveling (just wouldn't even power on; apple store replaced it).
Due to a pretty heavy schedule since then (lots of travel, lots of work, and night classes), I haven't had much opportunity to do anything extreme on my fancy new computer. Despite that, I have noticed it often feels SLOW. Like, really slow. Stuff like taking 2 seconds just to switch between open apps, when you only have 2 apps open (and I'm not talking Final Cut and Photoshop, I'm talking Safari and Mail). Numbers was barely usable, sometimes dropping keystrokes as I tabbed between cells (and switching cells took over a second). Pages was frustratingly slow. It was bad. Finally, I reached a boiling point when I downloaded the latest Humble Indie Bundle, and Jamestown (a vertical-scrolling, 2D shooter) was unplayably slow. It wasn't running at a consistently low framerate, but it would basically freeze up for a second every 3 seconds or so. That's a lot of freezing up.
Today, I ran Geek Bench, and compared my score to a typical sandy bridge MBP 17". Typical 17" was in the neighborhood of 11,000. My MBP17" scored in the neighborhood of 2700! That is pretty bad!
Anyway, I'm trying to figure out where to even look. I ran the benchmark with all apps closed. It wasn't a fresh boot, but trust me I've rebooted plenty of times and it's been noticeably slow every time. I download Onyx a week ago and had it clear out all my caches, refresh my prebindings, run the periodic crons, and also did a repair disk permissions from Disk Utility. None of that has brought my score above 3000.
When I say I ran Geek Bench by itself, that's not entirely true. I always set up Activity Monitor to be a startup app, minimized to my dock. It's always plenty idle. There are no visible runaway processes or memory hogs. I do have it set ot display All Processes. I also ran memtest with 4 passes to check if my memory was bad, and it found no errors.
I have Windows 7 in boot camp, and when I tried playing Jamestown there, it was fine. I've played some older games (like Mass Effect 1 and 2) earlier in the year in boot camp, and it seemed fine. Granted, those were older games. I haven't done anything that pushed it. I would consider my Windows partition to be "untested" in this regard--it hasn't proven that it's slow or not. Jamestown was playable and didn't stutter...but honestly that game would run well on my 4 year old 2-core MBP, which would probably score in the upper 2000's on Geek Bench anyway. That said, OS X does have a stuttering problem that doesn't seem to be happening in Windows.
I'm at a loss, and was planning to schedule a Genius Bar appointment for this weekend, but I'm curious if anybody has any insight or experience with this? I'll update the thread with whatever I learn at Apple.

Answer 1

Update: After I got home, I decided to do some more random troubleshooting. First I closed everything, did another repair permissions, rebooted and confirmed the performance was still slow.
Then I took my laptop out of the Book Arc stand (holds it vertical) and power-cycled the machine, now without my external peripherals. The Geek Bench now reported 10235! So that is good news!
Interestingly, my battery (despite having been plugged in for weeks) was at 0%, so it seems like there might be a problem with the SMC. I reset it and I'll see how it goes. Doing a Geek Bench run each time, I put my computer back in its stand and hooked it up to the external monitor and keyboard.
I tried the Jamestown test, and I was sad to see that even with good geek bench numbers, it was still herky jerky. I removed the laptop from the Book Arc and played on the built-in keyboard and display, and the problems were gone. I hooked it back up to the external display, and things were fine, then, too.
I'm going to keep an eye on the CPU (by occasionally running geek bench) as well as the state of the battery. I've had the laptop out of its stand less than three weeks ago, which would imply that this slowdown problem should be isolated to no more than that period of time, but I have been observing slowness for longer than that.
As of now, I have nothing to show at the Genius Bar, so I'm cancelling.