I've been trying to compile every complaint about each and every line in the MTA but I can't figure it all out. My purpose is so that a meaningful fantasy map can be drawn. Not a "wew let's draw lines wherever I feel!" map but one that would actually be worth putting the money and labor into implementing.
I'll update this as new comments are made (and quote you, obviously) and I'll start off with what I ride.
IRT 42nd Street Shuttle
IRT Broadway-Seventh Avenue
IRT Dyre Avenue
IRT Eastern Parkway
IRT Flushing
IRT Jerome Avenue
IRT Lenox Avenue
IRT New Lots
IRT Nostrand Avenue
IRT Pelham
IRT White Plains
BMT Fourth Avenue
BMT 63rd Street (not used!!)
BMT Archer Avenue
BMT Astoria
BMT Brighton
BMT Broadway
BMT Canarsie
BMT Franklin Avenue
BMT Jamaica
BMT Myrtle Avenue
BMT Nassau Street
BMT Sea Beach
BMT West End-
"No major problems. The West End's regular service, the 
, doesn't get overcrowded but it still gets pretty packed during both the AM and PM rush. This isn't an issue unless something on the Fourth Avenue line or further up lines creates a delay. Also, during the dead cold of the winter, the R68's occasionally discharge at 9th Avenue (that's the worst) and 36th Street. Not sure if this is more of a West End/Fourth Avenue issue or a Concourse yard issue. If the Broad St-Montague Tube connection ever gets repaired, maybe I'd run either the 
or 
to run West End Express to ensure that delays don't clog up the West End, but this might have crowding effects on the Fourth Avenue line." -YungMarxian
IND Second Avenue (not yet!!)
IND Sixth Avenue
IND Eight Avenue
IND 63rd Street
IND Archer Avenue
IND Concourse
IND Crosstown
IND Culver
IND Fulton Street
IND Queens Boulevard
IND Rockaway