With gigabyte boards the letters all stand for certain features. It's sort of an easy wasy to get an overall idea of what the board offers just by looking at the name.
D stands for Ultra Durable.. (All solid caps design)
S are the features Safe, Smart, Speed, SLI, Silent Pipe
Q for Quad features Quad Bios, Quad Cooling, Quad Triple Phase, Quad eSata, Quad Core Ready, Quad DDR2 Slots
So,
Q6 = Quad Bios, Quad Cooling, Quad Triple Phase, Quad eSata, Quad Core Ready, Quad DDR2 Slots
S5 = Safe, Smart, Speed, Silent Pipe, SLI
S3 = Safe, Smart, Speed
S2 = Safe, Smart
That's just an overview, as others have posted there are other differences between the boards but this shows what the letters stand for.