Third party software isn't really a problem. x64 variants of Windows (including Vista) have an emulation layer that allows all 32-bit software to run and to be honest I've never seen any user-mode software throw a tantrum because of it.
Device drivers is another issue though. However Vista is launched in a matter of weeks and with it comes new restrictions on WHQL signed drivers. The new rules require that every WHQL driver will have both 32-bit and 64-bit binaries in a combined package. Both drivers must pass the stress tests before the WHQL signing is given to the driver. This is a big incentive for those pesky hardware vendors to get their finger out.
I'd get Vista 64-bit. You'll regret it in 6 months if you don't. Sure you will probably have a couple headaches with drivers until late February but they'll just be annoyances rather than show stoppers on the whole.