In addition to the Key Bus routes, they should run the following buses as well:
9 City Point-Copley
(to serve parts of South Boston further from Broadway)
31 Forest Hills-Mattapan
(Very busy bus route, valuable connection of Forest Hills to Blue Hill Ave)
34 Forest Hills-Dedham Line via Washington Street OR
36 Forest Hills-Charles River via Belgrade Ave
(Debatable I know, but both these buses have significant ridership and this would give service to West Roxbury)
70 Central Square, Cambridge-Cedarwood (End the route at Waltham Square)
(Anyone who has seen this bus at night knows it's always packed)
86 Cleveland Circle-Sullivan via Harvard
(Gives Union Square, Somerville service and connects Harvard and Cambridge to Brighton)
88 Lechmere-Clarendon Hill via Highland Ave and Davis
(Connects Somerville)
89 Sullivan-Davis via Broadway
(Also connects Somerville but different parts)
104 Malden-Sullivan via Broadway (Everett)
(Similar to the 70, this bus along with its counterpart the 109 are ALWAYS packed at night)
240 Ashmont-Crawford Square, Randolph
(Similarly always packed at night)
441/442 Wonderland-Central Square, Lynn via Lynnway
455 Wonderland-Salem Depot via Central Square, Lynn
(These two are debatable too, but connecting Lynn to Wonderland should be a priority, these buses have healthy ridership, and a late night connection to Salem State and Salem Center would be a great thing. The 455 is preferable but the 441/442 should be a minimum, it is a rather quick route.)
While I know this service is more for and will appeal more to the late night party crowd, that doesn't mean it can't also serve the working class as well, which the 31, 34, 36, 70, 89, 104, 240 and the North Shore buses certainly would.
Edit: Added the 240