Okay, the last few things I discovered

Vsync with ATI is also not working for BoBII. Generally the thing seems to be that for applications that not nativley offer Vsync, ATI can't force it at least not on Win7 x64. You definitely want the D3DOverrider application that comes with the latest Rivatuner downloads. You can discard Rivatuner (for me, that is too detailed to play around with it) but the D3DOverrider is a separate application, installs no drivers, you just open it when playing a game and it keeps Vsnyc.
Flat Panel Scaling: I think it's the same with Nvidia as with ATI: On the Win7 drivers, the Flat Panel Scaling (GPU Scaling in ATI Terms) options are by default grayed out on the windows desktop. I used this option in XP to get BoBII menus (which are 1024x768) up to 1920x1200 so my screen would not constantly switch resolutions around between menu and 3d part of the game. But on W7, these were gray and unable to be selected.
The fix is to lower the desktop resolution BELOW your native LCD resolution, for example to 1920x1080, then the grey options become selectable. Once you set a scaling option, you can then return the desktop to full resolution, and the option will again be grayed out, but stick with what you selected. I read the same about NVidia, so it's likely something within W7.
TrackIR: I had installed v4 of the Software (for my TIR4Pro) and it was working fine with Thirdwire sims, but failed to recognize FS2004. I was tearing my hair out, v5 of the Software however worked fine. At the NP support forum we then discovered that you have to install the software using rightclick "run as administrator" on the setup. Then it recognized FS2004.
So, that's another important lesson: When you are installing applications in W7, even if you have admin rights, it never hurts to use "run as administrator" especially if the software is also adding drivers. Obviously TIR v4 did a very weird "partial working" install because some rights weren't given when I ran it as normal user in the administrator group.
For Burning Software, I now use Ashampoo Burning Studio 2010 (Free Version) which does everything including Blu Ray and Lightscripe. You get a free full version key from the Ashampoo website, which is yours forever. Nero has a Version 9 Lite also for free download from the website, but it lacks burning of iso images to disk.
I installed the VPN Software from my company network which is a pretty deep system-level app, using the Vista x64 download, and that one also works. So far Win7 really has not refused any program I threw at it.
Start menu weirdness: I like to sort my programs in my "All programs" menu by hand, so that I find what I need often at the top of the pack. Very early I had already disabled "Sort alphabetically" for the W7 menu (all these options are under taskbar-rightclick-properties-start menu).
Yet still, after a day or two, my apps would again be sorted by name. Until I figured out that there's another option "highlight latest installed programs" which also has to be disabled, otherwise everytime you add a new software, the whole non-alphabetical order goes to hell.
For mobile devices, I was pleasantly surprised: My HTC Touch with Windows Mobile 6.0 was instantly recognized when I plugged the USB Cable in, Windows Update downloaded the drivers and software, and it was synching with my Outlook in no time. For XP, it always was a bother since ActiveSync was not freely available as download, and it didn't always recognize the connected device either. Of course also no problems with iTunes and the iPod.
I finished setting up everything on sunday and did a full image backup to VHD on an external drive. This built-in W7 backup is slightly slower than Acronis (doesn't use as much compression on the files, so more to write) but works okay. I also test-started a recovery booting from the Win7 DVD, and that works - it loads a mini-windows where you can point to the external USB drive and apply the backup image to your hard drive, bringing the entire system to the state you last did a backup. Highly recommended if you have a small system/applications drive with lots of custom settings.
Performance-wise, the i7-860 continues to impress. Going by benchmarks, the Phenom X4 965 would have beaten my previous AMD 5000+ by max about 180% (for example in Armed Assault from 17 to 25 FPS), but the i7 seems to do triple the amount of work (Arma at 30+ FPS), and with very little heat.
So in summary: I totally changed hardware, I changed GFX brand, I changed OS and I went 64bit. By any common logic, that was pure madness switching so much in a single move. But the biggest issues actually came from the GFX driver, which I could have avoided by going with Nvidia. So the conclusion seems to be that switching from 32bit XP to 64bit Win7 is actually less painful than switching from Nvidia to ATI - and that says something about the usability of the new OS. And ZERO problems with x64, too.