I've been running Windows Server 2008 x64 on the server hosting this blog since September, and I've got a couple of thoughts on running 64-bit. I didn't plan to install 64-bit in the first place, but I had problems getting Win2k8 CTP 32-bit to install back then, so I tried 64-bit, which worked, and ended up with that. I've kept upgrading it, most recently to RTM last Sunday.
For some reason, that screwed up the network drivers for my MS Virtual Server machines, leaving them with no network. That combined with setting up a RAID1 volume for the OS on the server, made me reinstall the whole server instead of troubleshooting the drivers. And when I had the chance, I made the switch back to 32-bit.
So, why did I switch back to 32-bit?
First, I don't have more than 3 GBs of RAM on this server, so I don't really need 64-bit except for the "coolness" of running 64-bit.
Second, I've has some issues with application compatibility.
First out was DasBlog, the open source .NET blog engine behind this blog. They're using a date picker tool that didn't support 64-bit, which broke the admin interface. I was able to fix it by browsing forums, googling a bit and downloading the 64-bit version of the date picker. Not too hard, but still, it didn't work out of the box.
Number two was a bit bigger. I'm using SourceGear Vault (which is a very good tool, btw), as my source control system. It turns out that they support 64-bit (with IIS in 32-bit mode, I should say), but not on Windows Server 2008/Vista/IIS7. So I had no other choice than setting up a 32-bit Virtual Server just for this.
I haven't experienced number three first hand myself, but I know that (at least a couple of months ago) the SharePoint Server SDK was only available for 32-bit, whcih makes development a bit hard if you're running 64-bit.
Finally, it should be mentioned that I haven't had a single 64-bit driver issue, so things are going the right way.
So, my conclusion is: Unless you have more than 3 GBs of RAM, 64 bit is (apart from the "X-factor" of running 64 bit) little but just one more item on the list of possible causes if something's not working. I don't know about you, but I'd like to keep that list as short at possible.