I would always just spell it out saying "Eye Eye Ess," but my boss always calls it "Two Ess," like the II is roman numeral. I know it stands for Internet Information so it is not really numbers, but on the other hand it is a lot easier to say "Two Ess."
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I pronounce it "Eye Eye Ess" as well. To pronounce it "two ess" is moronic, even if easier to say.
Similarly I prefer to say "Ess Queue Ell" rather than "Sequel" but at least "Sequel" is closer to the mark to SQL than "two ess" is to IIS.
I say eye eye ess too, I don't really think you could call it anything else, aprt from the full proper name.