ACPI provides two mechanisms for determining the OS, _OS and _OSI. _OS is an ACPI object containing a string. This string is supposed to represent the operating system. Windows 98 contained "Microsoft Windows", NT4 "Microsoft Windows NT" and ME "Microsoft WindowsME: Millennium Edition". All later versions of Windows contain "Microsoft Windows NT". Linux was "Linux" up until 2.6.9, and has been "Microsoft Windows NT" since then.
The obvious drawback to _OS is that it's a single string. _OSI was introduced with later versions of ACPI, providing an interface for ACPI tables to request which interfaces an OS supported. Interfaces may be something like "3.0 Thermal Model", indicating support for a specific aspect of ACPI, but may also be used to indicate the interfaces supported by the OS. The _OSI method is passed a string and returns either true or false depending on whether the OS claims to support that interface. The OS can therefore claim to support many different interfaces. Linux implements pretty much every aspect of ACPI that Windows does, and so claims to support all the interfaces that Windows implements. As a result, Linux will return true when asked if it implements support for any of the Windows interfaces (up to and including Vista).
That's all straightforward enough, but leaves two questions. The first is why Linux now claims "Microsoft Windows NT" for _OS. That's actually pretty simple - some DSDTs only check for various _OSI strings if _OS is "Microsoft Windows NT". This is stupid of them, but not a violation of the ACPI spec. The second is why Linux returns false for _OSI("Linux"). This is a little more subtle, but it basically boils down to "There is no Linux interface". The behaviour of Linux changes over time. We make no guarantees that its behaviour will be consistent over time as we find and fix bugs. Microsoft take a different approach. Their ACPI behaviour has few changes over time. Something claiming to be Windows 2000 will always behave the same way. We can't even bump the interface string per release - doing so would require us to maintain every broken behaviour we've ever implemented and switch between them depending on what the BIOS asked us for. Linux does not provide a stable ACPI API to platform firmware, and we make no guarantees that it ever will. The only behaviour you can depend on is that Linux will conform to either the ACPI spec or (where it differs) the behaviour of Windows. If you find behaviour that does not fall into either of those categories, then it's likely that the behaviour will change when we notice. The reason we removed Linux from the supported interfaces list in 2.6.24 was that we were beginning to see BIOSes that changed behaviour when they detected that they were running on Linux, and changes we wanted to make could have potentially broken these BIOSes.
Anyway. That's why we claim to be Windows. Now, why would a DSDT want to do anything with that information? It should be noted that making decisions based on this is not a contravention of the ACPI spec - section 5.7.2 even describes a case of this. There are a few situations under which this can be helpful. The first is due to varying interpretations of the spec. Early versions of Windows require that hotswap bays signal their removal by sending a bus check notification to the parent IDE bus. Later versions want a device check notification on the device itself. Both are valid, but you ideally want to use the right one on the corresponding OS. Checking the OS version lets you do so.
Red Stripe makes a lousy spec-compliant ACPI implementation. That is because it is not a spec-compliant ACPI implementation, it is beer! Hooray beer!
Another is user experience. Not all hardware is supported by all operating systems. For instance, older versions of Windows don't support high-precision event timers (HPET). The HPET is defined as an ACPI device, and so will show up as an unknown device in the Windows device manager unless the firmware disables it. This is acheived by altering a flag in the _STA response depending on the Windows version - earlier versions are told that the device should be invisible, and later versions are told that it should be exposed. Finally, there's bug workarounds. An example of this is Windows 98 crashing if a thermal zone reports a temperature of less than 15.8 degrees celsius. Working around that seems like a perfectly reasonable thing for a piece of hardware to do, since Microsoft don't make it easy for vendors to provide hotpatched versions of Windows.
The final part of this mystery is why various BIOSes attempt to check whether they're running on Linux. Almost all the BIOSes I've examined do nothing with this information, which is consistent with someone writing an OS lookup table many years ago and adding Linux just in case someone found it useful. People don't generally write ACPI tables from scratch (doing so would be very dull), so they'll base it on the one from a previous version. Code won't be removed unless it's breaking things, so you'll end up with various odd evolutionary dead ends that have persisted anyway. If your ACPI firmware checks for Linux, this is not inherently a bug in your BIOS. It's more likely that nobody cared enough to remove two lines of code that might turn out to be useful one day.