iOS 2

• This is the software that was available until the release of the iPhone 3G, the model which preceded the 3GS. While it's possible that this version will run on the 3GS, it isn't recommended as it lacks many of the features and capabilities requires to use your 3GS to its full capacity. You would have to intentionally downgrade your 3GS to acquire this iOS, as all iPhone 3GS shipped with at least iOS 3.
  
  

iOS 3.1.3

• This is the most recent build of iOS 3. It came out with the iPhone 3 and passed a few update cycles before being replaced by iOS 4. It runs well on the 3GS as it was designed specifically for that phone.
  
  

iOS 4.3

• This is the most recent build of the iOS 4. It was designed specifically for use with the iPhone 4, but it still runs on a 3GS phone. Not all features available with iOS4 will work on a 3GS due to the hardware specific nature of some features, but it will benefit from such upgrades as multitasking, which was previously unavailable with previous iOS versions.
  
  

iOS 5

• Apple has committed to supporting the iPhone 3GS with iOS 5. Whether any future updates will work with 3GS is unknown as of August 2011, but if history is any indicator, the 3GS is probably nearing the end of its support with Apple as the immediately preceding generations of iPhones and iPods are already unsupported by iOS 4.3.