Any South American/Central American service is desperately needed. There are only 3 weekly A319s by TACA to SAL, everything else goes through ATL, IAH, MIA, or DFW. I would assume Aeromexico would be at BOS by 2005, when they would have 737-600s able to easily to BOS-MEX and the new SkyTeam terminal will be done. I would doubt CUN since there is limited service to several hubs from CUN, let alone making it O&D.
Domestically, every city can be easily reached through a hub, with hourly flights to ATL, DFW, and ORD. The reason BOS-MSY doesn't exist is that the route would be solely O&D, as both airports are (with the exception of WN at MSY) O&D. If anything, it would be a better bet that MSY service from the Boston area would be Southwest to either PVD or MHT.
European service at BOS has been decreasing a lot of the past 15 years. I would doubt MAD would be close to getting on the list, but who knows? A big part of the MAD picture would be if AA/BA goes through (if it does, then no chance of MAD-BOS). FCO would be a longshot, but with DL and AZ having large operations at both ends and a huge Boston Italian population, it could work, even a seasonal flight.
As for Asia, the only carrier I see is Korean Air, which served BOS until the economy went south. Same thing with SkyTeam for my projections.