Update 2009-08-06: This was fixed in Windows 7 RTM and is not longer an issue :)
For some time I had problems with StarCraft in Windows 7, after playing for 20-30min Windows 7 completely freezes keyboard, mouse and video (background programs and even Skype still work, but a hard reset was always the only way to get out of it). Since I was not playing much (just a few games a week) and it did not happen to me that much, I did not worry at first. But after starting to play ICCUP a few weeks ago with some friends, it just got annoying when I was crashing every 2-3 games. At first I was thinking maybe I overclocked way too much with my 4 Ghz, so I tried playing with normal 2.6 Ghz, but that did not make any difference. I also removed one of my graphic cards and tried playing on my primary screen instead of my third one. Nothing did help. It seems when closing all programs and making sure StarCraft only ran on one core (using the processor affinity setting in the task manager) the crashes occured less often, but I could not really fix this issue.
In Windows 7 Beta I also had some crashes (but usually not blue screens or whole computer freezes) with some games and applications, e.g. some Half-Life2 games like Garry's Mod or Left 4 Dead crashed a few times for me, but with WIndows 7 RC this did not happen anymore. In fact other than testing my overclocking settings I never had any crash or bluescreen in Windows 7 RC except for playing StarCraft.
After reading a bit on some forums (TeamLiquid, Blizzard, random Boards on the Internet) I saw many other people having the exact same problem: Windows 7 RC x64 + StarCraft does not work well together. In fact any other 2D DirectX from that time (like Age Of Empires 2, Worms Armageddon, etc.) seems also to cause random crashes in Windows 7 RC, especially on a quad core system. Some people also had another issue with the 256 colors, the trick here was to keep the Screen Resolution dialog open in Windows and then start the game.
Well, the solution is kinda retarded, but it seems to work (many people reported it and I did not have any problems since yesterday when I started using this trick): Kill the Explorer.exe process before starting StarCraft.exe and restart it only after closing StarCraft.exe again.
Since I also wanted to use the ICCUP Launcher, I wrote a little cmd script for this job. I also had to disable some of my programs like WallRotate to prevent the 256 colors messing up in StarCraft every time my desktop changes. Here is the .cmd file I use for starting StarCraft via the ICCUP Launcher.exe plus all the additional tricks like waiting 2 seconds for the update check of Launcher.exe, killing WallRotate.exe (I commented it out, replace it with any other program you might want to close too) and Explorer.exe and restarting everything after closing StarCraft again.
rem First start the ICCUP launcher (it won't work without Explorer.exe)
cmd.exe /C start C:\Games\Starcraft\Launcher.exe
rem Wait a bit for ICCUP Launchers update check! Use ping trick to wait 2 sec!
ping 127.0.0.1 -n 2
rem First kill Explorer.exe, which messes up our colors in StarCraft
taskkill /f /IM explorer.exe
rem Also kill our desktop changer, which messes up the colors in game
rem taskkill /f /IM WallRotate.exe
rem Change to the StarCraft directory to make sure we run normally!
rem And launch StarCraft ourselfs since we can't see the ICCUP launcher without Explorer.exe
rem Please note that /affinity 1 makes sure we only use our first core
rem Using all cores for StarCraft.exe can lead to crashes in Windows 7 :(
cmd.exe /C start /affinity 1 C:\Games\Starcraft\StarCraft.exe
rem Some early tests:
rem Wait for the game to quit, press Enter to continue
rem Restart Explorer.exe and WallRotate, that's it!
rem start C:\code\WallRotate\bin\Release\WallRotate.exe