Another reason that a lot of companies have not gone through the effort of creating 64 bit versions is simply they don't need to.
Windows has WoW64 (Windows on Windows 64 bit) and Linux can have the 32 bit libraries available alongside the 64 bit. Both of these allow us to run 32 bit applications in 64 bit environments.
As long as the software is able to run in this way, there is not a major incentive to convert to 64 bit.
Exceptions to this are things such as device drivers as they are tied in deeper with the operating systems and cannot run in the 32 bit layer that the x86-64/AMD64 based 64-bit operating systems offer (IA64 is unable to do this from what I understand).
I agree with you on flash player though, I am very disappointed in Adobe that they have not updated this product. As you have pointed out, it does not work properly in 64 bit requiring you to run the 32 bit version of Internet Explorer.
I think it is a strategic mistake on Adobe's part. Having to run the 32 bit browser for flash player is an inconvenience for users, and many will not understand this solution. This could lead to developers being apprehensive about using flash. The most important thing for a web site is to make sure everyone can view it, solutions that alienate users are typically not popular ones. Flash's popularity was fed by its own popularity, the more sites that used it, the more users had it on their systems, the more users that had it on their systems, the more sites were willing to use it.
The retail market pushes these things forward, when a general consumer goes to buy a new computer, they aren't going to know they don't need a 64 bit OS they are going to get it either because they hear it is the latest and greatest thing, the future of computing, or just because they don't know the difference.
Vista has been out for about 2 years now, and Windows XP 64-bit was out before that. In my mind that is too long for a major technology such as Flash to not be upgraded if they want to hold on to their market. It may have to do with Adobe taking over Macromedia and this is a sign that Adobe does not feel Flash is part of their future, I find it hard to believe as I think Flash and Dreamweaver were the top parts of what they got out of Macromedia, but then why have they not updated it yet?