Microsoft wants you to work the Web with Windows on your desktop. And that means if you are running anything besides Internet Explorer, you are going to have problems down the road.

Windows has become the best Internet OS. It just kills me, as I write this on my Mac running Firefox. If you want evidence of this, set up two equivalent PCs, or better yet, buy a Mac Core Duo and run both operating systems on the same box with one of the multi-boot options. Go out and surf the Web. And other than being infected with a bunch of spyware and toolbar download come-ons on Windows, you’ll find that pages load faster and you can get more work done on Windows.

Here are some other data points. I use Google’s Gmail as my main email application. On the Mac with either Firefox or Safari, it runs slower than on Windows with Internet Explorer. If I make use of OfficeLive to set up a Web site, I don’t have a choice. I must be running Windows/IE – that is the only way I can maintain my site and make use of the various “live” tools. (Forget about things like FTP.) The same situation is with Sharepoint, and LiveMeeting, and all sorts of other browser-based Microsoft applications. You need IE for this world-wide-Web thing. And if you need IE, you need Windows to run it.

I am finding that more and more of what I want to do with Microsoft requires me to be running Windows. I guess that has always been Microsoft’s no-so-secret plan — to do a better job than anyone else at making development tools and runtime environments for Internet applications. They have succeeded, even though the market share of IE has continued to slip over the past couple of years.

Take a look at what happened with Java on the desktop. Which desktop OS is the best Java environment, the most efficient place to code, the fastest performer? Windows! Microsoft took things seriously, and spent some time optimizing and extending Java so that it ran better on Windows. So what happened to Java being able to run everywhere? That’s so five minutes ago.

Now most people write their Java code on Windows development platforms, because wouldn’t you know Microsoft has some of the best development tools out there. So they code and test on Windows, and guess what? These apps run only Windows, and well, sometimes we’ll see a port over to Linux, and maybe we’ll get around to doing the Mac sometime next year if the customers yell enough.

Think of IE as the way Microsoft will move towards an all-Windows Internet OS. And it will get worse with IE7 and Vista.

IE7 should really be called XP/SP3, because it changes so much of the underlying Windows OS. It basically gets that XP desktop ready to do a few of things that Vista will bring to the table. And for those corporate customers that are testing Vista, they will have to formulate a browser transition strategy as well. The issue is not so much that people will want to run both browsers. It is that so much of our computing environment is now tied to a particular browser version — and now the Windows OS that runs that version.

First is the issue of infect-o-rama from IE versions past. All of us have seen good PCs go south with spyware, phishing sites, and who knows what. The average Windows user catches these demons just from surfing around the Web. (Not on my Mac, of course.) IE7 supposedly fixes this, by adding various security measures. I can’t tell you yet whether they really work, but let’s say they do.

Next is the issue that not all Web sites will appear correctly because IE7 changes enough things. After all these years of IE5/6 it is a big change and many things don’t work (yet, or will ever) in IE7. I can’t tell you the percentage, but I have heard anecdotal reports. So chances are, if you upgrade to IE7, you will need to use some other browser for these situations for the time being.

Third is that IE7 is only available for some Windows customers. You have to be running an updated and legal version of XP/SP2. You have to be willing to change your desktop over to IE7, because it isn’t easy to go back to IE6 once you have done the update.

Microsoft has already got this angle covered. They have developed a Virtual PC “appliance” (really, a disk image) that has XP/SP2 with IE6 all nicely bundled up together. You can download it for free here.

There are a couple of problems. First, you need XP Pro (not Home) to run Virtual PC. Second, you need a lot of spare disk space and oodles of RAM to set this up. Third, the disk image expires on April 1, so you better be done with your testing by then and ready to roll out IE7 into production. And while running IE6 in a virtual machine makes a lot of sense from a security standpoint, especially given all the security loopholes on IE, it still is a cumbersome way to test a new browser and does require a leap of faith that things will work on IE7. It might have been a better thing to create a disk image for XP/IE7 that doesn’t expire, and let people stick with IE6 on the regular portion of their PCs.

The problem is that customers are going to be buying new machines with Vista and IE7 already installed, so they are coming into your corporate house whether you like them or not. Microsoft has always said that the browser is part of the OS. We just weren’t really listening.

As Yogi Berra once said, “When you come to a fork in the road, take it.” Who knew that he was talking about Web browsers?