Actually, some of those Manhattan trips actually DO make the whole trip. Today's Bx12 SBS MJQ runs (#6107 and #6227) went from Bay Plaza to Inwood, and started again at Fordham Plaza heading Bay Plaza. But yeah, most of them are short turns.
If I could fix your list up a bit, the typical weekday trips actually look like this:
Bx1/Bx2 (MJQ) - Mott Haven to and from Fordham Rd
Bx3 (MHV, MJQ) - Washington Heights to and from Kingsbridge Road (a few trips go up to Riverdale)
Bx4 / A (WF) - Usually interlines with the Bx40 / 42 trips
Bx9 (WF, MCH, OH) - West Farms / Riverdale to and from 225th Street & Bway (The trips will often run from either end of the route to 225th and then go back, or will just make the entire trip)
Bx12 / SBS (MJQ, MHV) - Usually make the whole trip but some trips end at University Avenue or Fordham Plaza
Bx15 (WF, OH) - 149 st to and from Fordham plaza
Bx28 (MHV, MCH) - Co-Op City to and from Norwood, with some trips going all the way to Fordham Center (the first day these loans started, an XD60 from OH ran on the line)
Bx41 / SBS (WF, MCH) - 149st to and from Fordham Plaza
Bx40 / 42 (WF) - Whole route
The weekend loans are a lot more interesting. One weekend, Staten Island did some trips. Another weekend it was Manhattan, and last weekend it was West Farms (an XN40 ran on the Bx7 and on the Bx28).