Ok, I've got great news for some of you. I've got a macpro (early 2009). After upgrading to 10.8.2 and changing the energy saver preferences to use the wake on ethernet option, I've had the un-wakeable sleep problem and its driven me nuts the past week!
I suggest you all carefully look at your /var/log/system/system.log file, as well as the /var/log/DiagnosticMessages/{date}.asl file. (you can read those with syslog -f {filename}). That is how I traced down the source of my problem.
So here's my situation. My monitors would sleep at exactly the time interval specified in energy saver preferences, note that the status light next to the powerbutton would stay solid. Then computer would then sleep roughly the time I expected it to, but rarely at the exact time. Anyways, after going to sleep, I'd hear a click and the status light would go from solid to the heartbeat thing. After reviewing the system.log, I noticed that precisely 2 hours after sleeping, the computer would go into a maintenance mode. You'll see this in the system.log:
Oct 26 14:51:25 MacPro kernel[0]: Wake reason: RTC (Alarm)
Oct 26 14:51:25 MacPro kernel[0]: RTC: Maintenance 2012/10/26 21:51:24, sleep 2012/10/26 19:51:27
Oct 26 14:51:25 MacPro kernel[0]: No interval found for . Using 8000000
Oct 26 14:51:25 MacPro kernel[0]: Graphics suppressed 0 ms
Oct 26 14:51:25 MacPro kernel[0]: Previous Sleep Cause: 5
Oct 26 14:51:25 MacPro kernel[0]: Intel82574L::setLinkStatus - not active 1face000, 0
Oct 26 14:51:25 MacPro kernel[0]: Intel82574L::setLinkStatus - not active 1face001, 0
Oct 26 14:51:25 MacPro kernel[0]: Intel82574L::setLinkStatus - not active 1face000, 0
Oct 26 14:51:25 MacPro.local configd[17]: network changed: v4(en1-:192.168.1.239) DNS- Proxy- SMB
Oct 26 14:51:25 MacPro kernel[0]: Intel82574L::setLinkStatus - not active 1face001, 0
Oct 26 14:51:28 MacPro kernel[0]: Ethernet [Intel82574L]: Link up on en1, 1-Gigabit, Full-duplex, Symmetric flow-control, Debug [796d,af48,0de1,0200,c5e1,3800]
Oct 26 14:51:28 MacPro kernel[0]: Intel82574L::setLinkStatus - active 1face001, b
Oct 26 14:51:32 MacPro.local configd[17]: network changed: v4(en1+:192.168.1.239) DNS+ Proxy+ SMB
Oct 26 14:51:34 MacPro kernel[0]: Intel82574L::timeoutHandler - no link - reset the chipset once 1face000, 0
Oct 26 14:51:34 MacPro kernel[0]: Intel82574L::setLinkStatus - not active 1face000, 0
Oct 26 14:52:05 --- last message repeated 2 times ---
Oct 26 14:52:10 MacPro kernel[0]: NVDA::setPowerState(0xffffff801df17000, 0 -> 1) timed out after 45476 ms
Note the 4th line, where it says graphics suppressed, then the last line where it says NVDA:: .... timed out.... That was the clue I needed. It seems that this maintenance mode wakes up to turn on the network interfaces, but tries to suppress the graphics card from waking up... However, the graphics card just times out. Apparently it doesn't support this action very well. I carefully watched my system and precisely 2 hours after it goes to sleep, I hear the system click, and the status light would go from heartbeat to solid.... Thats when the system freezes and you can no longer revive it. Actually, to be clear, the system was still accessible by ssh, so more accurately I'd say that probably it was just the graphics card was frozen... Nothing but a reboot would fix it. Note that I even tried issuing a reboot via SSH (thinking that was slightly safer than just holding the powerbutton), and although it did shut down some services (like SSH) it wouldn't complete the reboot and I'd still have to hit the Power button....
So anyway, now that I was pretty sure it was graphics card related (and triggered by the maintenance mode apparently related to the wake-on-lan), I googled 10.8.2 and nvidia... and what do you know? Nvidia released new drivers specifically for 10.8.2 this month!
This is the driver I needed for my stock GeForce GT 120:
http://www.nvidia.com/object/macosx-304.00.05f02-driver.html
PLEASE read the notes, it says its that this particular driver is for MacPro's only and 10.8.2 only.
Possibly check for drivers for other nvidia cards if this isn't you!
http://www.nvidia.com/Download/index.aspx?lang=en-us
So I installed the driver, rebooted, and voila, all works fine. I let it sleep, it went into maintenance mode after sleeping for two hours, and this time the monitor came on for 30 seconds, then went back to sleep (again with the heartbeat). I could issue a wakeonlan signal and then ssh in, or I could wake the computer by pressing the power button briefly. From my perspective, all is working fine. I can wake it properly from the power button, and I can wake-on-lan it properly too.
And just for reference, I use this wake-on-lan perl script. It works great, even through a router and wifi.
http://gsd.di.uminho.pt/jpo/software/wakeonlan/
I didn't realize this at first, but when sending the wakeonlan through a router you don't specify the IP address of the computer you're trying to contact. Just use the default ip (255.255.255.255 or your local network broadcast ip, like 192.168.1.255). The problem with routers is that once you're computer sleeps the router forgets your computer, so you need to broadcast the message to ALL ips and wait for the right one to match the macaddress and wake up... So just run it like "wakeonlan <macaddress>" and it works perfect. It even wakes my macbookpros connected only by wifi.
Also note that I tried the "darkwake=0" thing as well. I'm not really sure if that made any difference, but it is still set that way on my machine. You may or may not need that, I'm just not sure.
And one last note, I called applecare thinking my macpro still had coverage, but it turns out it expired a few months ago. They had me explain the problem anyways and said this is a "known issue" and that they could fix it for $59 or whatever. I told them no and figured it out on my own, but, it kinda ****** me off considering this was NOT really a hardware problem. It was an issue introduced by OS X 10.8 and I just recently PAID for this O/S upgrade. Personally I think they should be supporting this since I bought the O/S. My hardware was fine, it was the stock graphic card drivers bundled in 10.8.2 that was the problem! I fully assume that a future upgrade (maybe 10.8.3 if you're lucky) will include the updated drivers... Until then they're happy to NOT publish this simple fix anywhere and charge you for it instead. VERY LAME APPLE!
Best of luck to the rest of you. If this doesn't solve your problem, check those log files I pointed out, try to pinpoint the time your machine freezes and look for related events in the log files!
Cheers,
Rob