Here is an attempt at a brief summary.  I hope not to slight anyone's favorite

Historically, the greatest railroad development was around the time of and
just after the [American] Civil War of 1861-4.  After the war, the South
was a wreck, of course.  Previously, the 4 largest cities west of the
mountains were (not necessarily in order): New Orleans, St. Louis,
Pittsburgh, and Cincinnati.  Not at all coincidentally, all lie on the
Ohio-Mississippi River system.  All but Pittsburgh lost out in a big way
after the war, being right on the border of (Cinci.) or actually in
the area of fighting.  Chicago, a village of barely over 1000 people,
began to grow enormously, as did Pittsburgh, Cleveland, Detroit, etc.
from the war effort (the 1960s-1980s "Rust Belt").  Thus, rail growth 
centered on the East Coast -to- Chicago corridor.  This meant Boston,
New York, Philadelphia, and Baltimore (and to a lesser extent, Norfolk,
Virginia) to Chicago primarily, to St. Louis secondarily.  From this
came the largest 2 railroads in the US, the Pennsylvania, and the
New York Central.  Both started in the East, consolidated feeders
into large, 4-track main lines across their respective states, and
began splitting into feeders again across Ohio and Indiana before
reaching Chicago and St. Louis.

With similar ambitions, but farther south, Baltimore & Ohio, 
Chesapeake & Ohio, and Norfolk & Western reached from the east coast
to the midwest.  Despite their charm, though, they remained 2nd-rate
carriers in terms of volume, and none of these had much triple trackage,
let alone 4-track territory.  Reading, CNJ, Lackawanna (DL&W), New Haven,
Boston & Maine, Delaware & Hudson, Erie remained pretty much regional
carriers (though Erie reached Chicago via a terribly circuitous route).
New Haven had extensive 4-track territory because of passenger density
(Connecticut residents commuting to New York) but not nearly as much as
NYC and PRR.  The others had bits and pieces of 3-track and were otherwise
2-track and 1-track railroads.  [Incidentally, I'm speaking of main
lines only in giving numbers of tracks and some idea of traffic density.]

Illinois Central, Jon's favorite, stands out as a rare north-south
railroad, connecting Chicago with the Gulf of Mexico.  In the southeast,
there were the Southern (SOU), N&W, Seaboard Air Line, Atlantic Coast
Line, Louisville & Nashville.  All 1- or 2-track main lines in a web
covering the South.

Both in the North and the South, the Mississippi is a traditional dividing
line between the eastern and western roads, to a great degree even today.
Main lines in the West were essentially east-west things go get across
the great expanse of 'wilderness' to the West Coast.  From north to south,
roughly, there are:  Great Northern (via Minnesota and Montana);
Northern Pacific (nearly ditto, a bit to the south);  Chicago North
Western - Union Pacific - Southern Pacific (via Iowa and Nebraska);
Santa Fe (AT&SF) (veering to the southwest through Kansas, New Mexico,
et al.);  and Southern Pacific (New Orleans, across Texas to Calif.)

Kansas City Southern and Denver & Rio Grande Western were near their
namesake cities; MoPac, Missouri Pacific, was near its namesake state
in the midwest.

Today, there have been many consolidations in to basically 5, and possibly
soon 4, large regional carriers.

Early 1960s, DL&W + Erie = EL.  Also, N&W grew in 1964 by addition of
Wabash WAB and "Nickel Plate" NKP (regional midwest carriers) but stayed N&W.
ACL and SAL consolidated to SCL.

In the northeast, PRR+NYC, +later NH, made PC, which went bankrupt in 1970,
the largest bankruptcy until Chrysler beat them out.  With RDG, DL&W, Erie,
(last 2 by then made EL), and smaller lines created Conrail (CR) in 1976.

In the northwest, GN + NP + CB&Q (Chicago, Burlington & Quincy) made
Burlington Northern, BN.  This was mid-1970s?  Late 70s?

In the South, SOU + N&W in the early 1980s made Norfolk Sothern.  B&O and
C&O were already associated, then with Western Maryland (a regional)
created Chessie system.  Then with SCL and L&N created CSX (just CSX,
letters don't mean anything really...).

Thus there were 7 (I think) relatively large systems through the late
1980s to the early 1990s and things looked pretty stable.  In the
east, there were CR (now out of bankruptcy and Federal ownership),
CSX, and NS; in the West, BN, UP, ATSF, UP.  The next tier were IC,
KCS, MP (MoPac), etc., the larger regional carriers.  Though NS almost
got away with buying CR from the Feds.

Then ATSF and SP nearly pulled off a merger, and actually started merging
upper corporate structures (holding companies), but were forced to
split when regulators did not approve the merger.  This prompted BN and
ATSF to marry into BNSF.

Then UP started gobbling up anything else with the word "Pacific" in it
while magically keeping its identity, colors, and arrogance.  Thus, UP + 
Western Pacific + MoPac became UP (I), then + CNW became UP (II), and
now most recently with SP became UP (III).  

And now after a long fight, NS and CSX look poised, pending final
approval, to split Conrail basically along its old PRR/NYC lines, into
bigger, better NSes and CSXes.


The western roads essentially follow the General Code of Operating Rules,
GCOR.  I don't know whose rules predominantly shaped that rulebook.
In the northeast, there were so many problems caused by the devolution
of small rail lines to regional carriers or commuter authorities, causing
many situations where engineers would have to pass rules tests for 2 or
sometimes 3 or 4 railroads, that Conrail and Amtrak got together with
the smaller carriers to form NORAC, Northeast Operating Rules Advisory
Committee to draw up a common set.  (THis common set required even some
of the major players to change many signals, e.g. when the meaning of
Y/Y was changed.)  In the southeast, CSX and NS run with their own,
independent rule systems.  For signals, NS is quickly phasing out :-(
the N&W color-position signals.  CSX currently has the B&O-style
color-position signals which are being phased out, plus the C&O-style
and SCL-style color-light signals, which are incompatible (aspect-wise)
with each other (and with NORAC, which they are soon to absorb..)
The bigger incompatibility, though, is NS's route signalling orientation
versus NORAC's near-total speed orientation.