How about the short tunnel which connected the 9th Av. El to the Jerome Av. line (Sedgewick Av.). In the broad sense it is a subway but to the purist it is part of an el. It is disconnected at both ends and therefore abandoned.
That tunnel is still there, HOWEVER, the Anderson-Jerome Av side has been sealed (with concrete) and the Sedgewick Av side has been sealed as well (locked steel gates). Additionally the overpass that would bring you close to the Sedgewick station has been completely fenced off.
Actually, both sides are concrete-sealed. This is one of very few tunnels in NYC that, so far as I know, is completely sealed up and never inspected. I read an article where the MTA disavows any ownership of it (which I can't imagine is true). One day 100 years from now maybe the street above will have a large sinkhole and something will be done...
As for other tunnels, there are no outright abandoned sections of subway tunnel, but there are small inactive segments. There's the 'dust tunnel' between manhattan bridge approaches that closed with the opening of the christie (sp?) st. connection, a small piece of the ole trolley loop on the 7 line, and the chinatown segment of SAS which will likely never see a subway. There's a few real mystery tunnels too - such as LOMEX (which is on at least one internal MTA map), and the infamous 76 st. tunnel mystery (which is a huge can of worms).
There's lots of photos of some of these obscure spots on this page:
" onclick="window.open(this.href);return false;