The article about a lack of 64 bit software doesn't really suggest *not* upgrading, it just shows (truthfully) that upgrading doesn't get you a lot of improvement in your apps, depending on what apps you use (in the 3D industry 64 bit apps have been available for several years now in many cases). However that doesn't mean it's not good for other reasons to upgrade, especially since 32 bit software works virtually without a hitch. The access to more memory alone is worth it.
Most of the problems people have had, particularly in XP and lingering through Vista, were issues of driver support, not software support. And those are legitimate issues. I've used 64 bit versions of Windows since XP x64, and it's gotten a lot easier with each version. Even XP was quite usable, you just felt a little more limited in terms of hardware options, so you sometimes had to choose carefully. For those using high-end graphics apps though it was worth selecting the right hardware so they could get 8GB or more of RAM into their rendering workstations.
Once Vista arrived, a lot more 64 bit drivers came on the scene and the 64 bit versions of Vista were a lot more visible and available too (recall that XP x64 was a later release, never something you could purchase in a store at retail, and even on MS's site was hard to find info about). Now with Win7 it's even more mainstream and, as others have said, 64 bit OSs are starting to ship as the main OS for many newer systems, which is as sure a sign as any that it's probably ready for "prime time". You can bet manufacturers aren't going to be installing a 64 bit OS for Average Joe if they know he doesn't *need* it and they feel it increase support costs and problems.
Honestly I think the Windows Secret article is just trying to stir up some trouble (and page reads) based on older user fears. That being said I can't read the article as I'm not a subscriber.

But I *do* know that Windows 7 64 bit is pretty much problem-free, or at least no more problematic than the 32 bit version.
- Oshyan