There are a number of decisions to be made when modeling a station, and the most important one is the track plan of the station as the track plan will undoubtedly influence the overall layout track plan. Station track plans can be generalized into three different categories: Through, Stub, and Combination.
The above track schematic is of Penn Station in New York City and represents a classic example of a "through" station. The mainlines pass through the station from New Jersey and Philadelphia towards New England and Long Island, hence the categorization as "through."
Through stations have the advantage of being very easy to incorporate into a layout with an oval traack plan. Oval track plans also allow trains to continuously run around the oval, while not prototypical, certainly is nice to watch. Through stations often have a bypass track(s) with no platform(s) for freight trains and expresses to pass through station without stopping. When building through stations measures must be taken to keep minifigs safe as they change platforms.
The above photograph shows a board crossing between platforms, which can be used for stations with limited train traffic. It is easy to build with brown plates or tiles, however minifigs must take care when crossing active tracks. Also note the yellow safety border on the platform.
Another option which will keep minifigs safer are subterranean crossings under the tracks. The photograph above depicts a "dummy" crossing (i.e. there are no stairs in the stairwell). Dummy subterranean crossings are also easy to build. A nice addition might be a lamp or clock on a post where the 1 x 1 cones are.
However, as seen above, dummy stairwells are not very convincing when viewed from directly above.
Elevated walkways provide more visual interest, but necessitate bulding stairs.
Through stations (in fact stations in general) do not have to be at the level of the tracks, stations can be built above the tracks or below the tracks with stairwells leading to the platforms. The above two photographs show a station built above the tracks (kitbashed from set 2150) with dummy stairwells leading down to the platforms.
The above track schematic is of the lower level of Grand Central Station in New York City and represents a classic example of a "stub" station. The mainlines coming in from New England and upstate New York terminate in the station, hence it is a "stub."
"Stub" stations are challenging to operate due to the need to turn around trains to leave the station; most prototype railroads avoided this design, however stub stations were often the design used as the end-of-the-line station. In order to turn around trains, a wye, reversing loop, or turntable was often required. The Grand Central track plan includes reversing loops running under the main waiting room and are seen on the far left of the track schematic. The above photograph shows a turntable and roundhouse (kitbashed from set 10027). Layout track plans with stub stations require additional space for wyes, loops, or turntables.