Transportation to Disney Resorts will continue to run until the MK is clear of ALL guests. Disney won't leave you stranded.
As for Fort Wilderness/Wilderness Lodge... for special parties, they will typically run 45 mins after the party ends. (However, they will NOT run for E-Ride nights)
As for the Bethany shuttles to the Downtown Disney resorts... you will have to doublecheck with them specifically, however, in the past, I have seen them picking up as late as 1:45am... You'll want to double check with them as to when the last bus is...