The S50 uses an circa 1989 805cc, high compression, high-reving twin carb motor originally found in the VX800, a standard that looked like a naked sportbike that was canceled after only three years. The motor was too good to drop so it went into the Intruder 750 frame to make the Intruder 800, which had its name changed to S50 in 2005. A great bike, but it sells poorly now, and it is expensive to produce because it does not share a motor or frame (or really anything else for that matter) with any other Suzuki model.
The C50 uses a lower compression engine designed in 2000 or so. The C50 motor is also 805ccs for marketing reasons, but shares no parts with the 805 from the Intruder. It originally had a single carb back when it was called the Volusia, when meant that the rear cylinder is backwards compared to the Intruder or Marauder 805 motors. It is physically fatter to look like a bigger displacement motor that it is, and makes power at lower RPM, and has different gearing in the tranny to match. It was updated with fuel injection when the Volusia was renamed the C50 in 2005.
The M50 uses a more blacked out version of the C50 motor developed in 2004, with different valve train, ever so slightly different heads, and different cases (not just because of the color but also because the main bearings are a different design). It uses the same fuel injection system and electronics as the C50, and power is identical. This motor goes away, and the M50 will now use the same exact motor as the C50, reducing production costs and simplifying logistics at the factory.
The C90 uses a 1500cc motor that dates to 1997, and was loosely based on the discontinued Intruder 1400/ S83 motor: air cooled with a system that pushes oil through an oil cooler and then sprays it onto the bottom of the pistons for additional cooling. Originally built with two carbs, it gained fuel injection when the name was changed from Intruder 1500LC to C90 in 2005.
The M90r uses a brand new water cooled motor, basically a scaled back version of the M109r/ C109r motor. It revs higher, has more valves, and flows more air, and makes more power then the current C90 motor. Suzuki plans to kill off the old C90 and build a new C90r, which will use the M90r motor in a more 'classic' looking, full fendered bike (along the same lines as the C109r or the C50).
So that will leave three motors, in 800, 1500, and 1800ccs. Each motor size will be found in three versions: an aggressively and muscularly styled "M" with Suzuki's distinctive headlight cowl; a full fendered classic "C" cruiser; and a "T" version of the "C" with windshield, saddlebags, floorboards, and other touring touches. Suzuki gets nine models out of three motors and three frames by changing the fenders, wheels, and some other bolt-on items. Great way to get the most from their development money, and a great way to consolidate production and save money by sharing as many parts between models as posible.