I have a model subway system in HO scale in my family room, freelanced but loosely based on NYs. It was/is my first layout, and subway modelling is actually one of the easier types of RRs to model, in my opinion. I'm not a master modeller by any means, but over time, you learn some new things and with a little imagination and strategically placed things, you can make a layout look pretty realistic.
I have a two track main line with some express passing sidings. The mainline has 1 island platform based station along the main line and 2 other island type platforms forming transfers to other "lines". The portion that runs in subway (tunnel lights and grafitti included) is nearest the back of the layout, with a strategically placed viewing area down the mouth of the tunnel. Even put some small areas of open cut into it. The rest that runs "outside" is either open cut or just open (for the moment, like any model RR, it's NOT done yet). I'll also have a 3 track, 4 train underground storage yard once I put the street down! Trains are no more than 4 cars (each car maximum 75' HO scale) long.
I have a major transfer station that uses Stillwell Ave as its basis. I modelled what I think Stillwell Ave would be like underground. 1/2 the station is underground (with one track having a complete subway approach -neat to watch), 3 tracks having cutaway underground approaches and 4 tracks having open cut / outdoor approaches. 2 approach tracks fan out into 7 tracks with island platforms, one track has its own subway tunnel approach. 5 tracks can handle the 4 car trains, 2 tracks can handle 3 car trains and 1 track can handle a 2 car train.
I was able to get lots of track into this layout and put some of it underground so I have lots of "rush hour" scenarios I can run through and the layout doesn't necessarily look like a maze of spaghetti.
One city / borough / metropolis is complete. It runs 2' x 8/5' over the tracks. Lots of buildings growing into skyscrapers the further back into the layout that you look. (N scale Atlas glass skyscraper kits work GREAT in HO scale!) Layout is on 2 tables, one 4' x 8'; the other 4' x 6' - a one foot wide "shelf" forms a bridge between the 2 tables.
Rolling stock is mixed: 2 trains of R-1/9s, 2 trains of BMT standards, 3 trains of San Francisco BART cars, 2 trains of WMATA cars, 1 train of R-15s and one "new technology" train of 3 WMATA cars repainted to resemble the 1980s standard MTA silver/blue scheme. Cut up subway maps for signage and even included this on the trains. Used standard Atlas components and track to electrify the whole thing. Used the Atlas "how to wire your layout" book to learn the wiring techniques. It ended up making a modern looking switchboard, in retrospect.
Underground stations are lit. Passengers gotta see :) Litter on tracks in stations. Some tracks have drainage ditches ala New York. Hanging signs from ceiling and small signs on steel beams. Tunnel walls grafittied. Stillwell Ave tiled wall is somewhat grimy but otherwise clean. Station platforms "comfortably crowded" with people, thanks to a fluke buyout of HO scale people at a "just a buck" store a few years back. Streets also fairly crowded because of another "just a buck" sale (2 HO scale cars for $1.00. Bought them out!) Working streetlights (some purposely out), non-working hanging traffic lights (amazing what a little black thread can do), scratchbuilt subway entrances using Atlas / Model Power gate kits.
Wish I can run it more often than I do!
Anyway, this oughtta give you some ideas to get started.
--Mark