It turns out that there's another hitch in estimating how crowded the subways are: in my last post I used the NYMTC's estimates of space per passenger from Table 20, but in the comments threestationsquare pointed out that they assume that every subway car has 602 square feet of space, which is definitely not true. Andrew suggested using the MTA's rush hour loading guidelines, which can be found on pages 26-31 of this PDF, and threestationsquare went with that. He also used the crowding in the 8AM hour, which makes sense since that's the peak hour for every line.
I'm on record as to the problems with loading guidelines. Capt Subway, who was a scheduler at the MTA for many years, added to my critique with his experiences, which are definitely worth a read. But the problems that the Capt noted are with the way the MTA measures compliance with the guidelines, and these are independent measures by the NYMTC. As Andrew noted, the rush hour guidelines are nowhere near as political as the off-peak guidelines, so I'm comfortable with that.
In every measure, however, the #7 train and the R have always been at the low end. This means that the capacity added in Long Island City has been a good thing, although as others have mentioned, a lot of people have moved into new apartments there since the fall of 2012, and more will come with Hunters Point South. There may not be any room left on the train by the time everything currently in the pipeline is built.
The J/M/Z and the 2/3 seem to have switched places, notably, so the zoning reforms should go in southern Bushwick rather than in Brooklyn Heights. But because there's still room on the R, we should allow some more residential development near Metrotech.
The Central Park West locals are an interesting challenge. As Jarrett Walker noted, when the "area served" by your station is half parkland or water, you need double the density to serve the same number of people - at least during the morning rush, when very few commuters are coming directly from Central Park. In consequence of the 2007 downzoning hysteria, that's not likely to happen soon. One thing that could help would be better crosstown bus service, so that more people can transfer from the bus.
It looks like, from the point of view of subway crowding, there isn't enough room to extend any of these subways. There may be the potential to reduce headways (which deserves its own post), but if not, I don't think it's worth a major capital investment if the rush hour loading is over 75% of the guidelines.