One point that I don't believe has come up yet, but should be mentioned, is that, if you buy a normal retail (It should also apply to MSDN/AA keys as well, but OEM versions are still sold in seperate 32 and 64 bit packages afaik) copy of Windows 7 (upgrade or full, makes no difference), you actually get both 64-bit and 32-bit media in the box meaning you can install 64-bit (which, as mentioned previously, should be your first call if your CPU supports it and you have 2GB or more RAM) to start with and, in the event something doesn't work, can easily downgrade to 32-bit. If the misbehaving apps aren't games, and you're prepared to fork out for 7 Pro, then you can try XP Mode, which MS recently made compatible with both VT and non-VT enabled CPUs, but it's worth the price hike over Home Premium on its own.
As for application and hardware compatibility, I've been running x64 7 since the beta and, aside from the typical new OS teething issues early on, it's handled everything I've thrown at it more or less. If your experience with 64-bit OSs has previously been with Linux, XP or even Vista, then I highly recommend you give it another chance with 7.