11 December 2012: Added information and photographs on the F-4S provided by Jan Jacobs and Rick Morgan
F4H-1F (F-4A): The first 47 F4H-1s were redesignated F4H-1F (and subsequently F-4A) in May 1961. Although the more or less official reason was that these had the 5/10 degree inlet ramps and were powered by the J79-GE-2 engine (the F suffix indicated a engine change), I'm not sure that there weren't some retrofitted with -8 engines or that flew with the 10/14 degree ramps and/or -8 engines for test purposes. For sure, you can't tell an F-4A by the flat canopy (only the first 18 had it) and small radome. There were F-4As with the flat canopy and the big radome and the raised canopy and the big radome. See http://tailspintopics.blogspot.com/2012/11/f4h-1-large-and-small-radomes.html for a list of my posts on the F-4As, one of which includes a summary of the various configurations of the F-4As by Bureau Number.
F4H-1 (F-4B): The "real" F4H-1 production began with Block 6 (Block numbers were used to designate production configuration*), starting with Bureau Number 148363 .
There were only a handful of notable external changes to the F-4B (as it was redesignated in November 1962) during its service life. These included the low-speed lift improvements, the bulges on the top of the wings over the main landing gear struts, and the ECM stuff added during the course of the Vietnam War.
Although developed for the heavier F-4J, the low-speed lift improvement package that consisted of the drooped ailerons, slotted stabilator, and elimination of the inboard leading edge flap was of benefit to the F-4B as well. It was incorporated on the production line beginning with F-4B Block 26, the first of which was BuNo 152995 that first flew in March 1966. It was retrofitted to most of the surviving earlier F-4Bs over time. For more on this, see http://tailspintopics.blogspot.com/2011/09/f-4-flapstabilizer-change.html
The addition of the strengthened main landing gear was reportedly accomplished in conjunction with the lift improvements. However, according to the McDonnell Plane Captains Handbook dated January 1970, it wasn't installed on the production line until BuNo 153912, which was the last but three of the production F4Bs; those delivered before then were modified at the next overhaul. The longer stoke oleo required a fairing over the landing gear mounting point on the upper wing surface.
You're on your own with respect to the ECM configurations, external strengthening doublers, the USMC RF-4B, etc for the time being.
The F-4C/D/E were U.S. Air Force variants. The F-4F was delivered to the German Air Force. The F-4G designation was applied to two different F-4s, a dozen built for the Navy with a data link and automatic carrier landing system (see http://thanlont.blogspot.com/2011/07/look-no-hands.html) and subsequently designated as F-4Bs, and a U.S. Air Force version specialized for air defense suppression. F-4H (supposedly too similar to the original F4H) and F-4I ("I" could be confused for "1"?) were not used.
The F-4J was the Navy's next Phantom, which flew for the first time in June 1966. The major changes were the deletion of the infrared tracker under the radome, the bulged wings to accommodate the larger tires introduced with the Air Force F-4C, an additional fuselage fuel cell, and the incorporation of an improved radar and an uprated J79, the -10. As it happened, neither the radar nor the engine were available on schedule, so the first F-4Js were delivered with ballast in the nose and -8 engines. These were known as the lead-nosed Js; most were delivered to the Blue Angels. (As a result of attrition, the Blues eventually flew at least two Js with -10 engines.)
The J79-GE-10 had a notably different afterburner. See http://tailhooktopics.blogspot.com/2011/11/j79-afterburner-nozzles.html. As far as I know, the -10 was not retrofitted to any F-4B.
The F-4K and F-4M were the British Phantoms, powered by the Rolls Royce Spey engine instead of the J79. These had bigger inlets, a wider fuselage, a deeper fuselage under the afterburners, an additional auxiliary air door on the upper aft fuselage, all to accommodate the larger Spey engine. The F-4K also had an extra extendable section on the nose landing gear strut for launch from the smaller British carrier. See http://tailhooktopics.blogspot.com/2012/05/spey-powered-phantom-changes.html
For various reasons, not the least of which was attrition during the Vietnam War, the F-4Bs went through a service-life-extension program, becoming F-4Ns. In addition to replacement of the wiring and other product improvements and repairs, the Bee Line brought all the selected F-4Bs up to the latest basic configuration, including the lift improvements and the strengthened main landing gear. The first F-4N flew in June 1972.
Note that early Ns did not get the long ECM-associated fairings on the top of the nacelle inlets as shown above (the one on the J was about half that length for some reason), so it isn't a certain indication of an N. This N is an example of that:
https://tailspintopics.blogspot.com/2017/08/f-4-phantom-acls-radar-reflector.html and http://thanlont.blogspot.com/2011/07/look-no-hands.html
Like ''I", "O" wasn't used for a modification letter and I don't know what the F-4P or R were to be.
The F-4S resulted from a service life extension program for the F-4J. It also featured the substitution of maneuver slats for the leading edge flaps. See http://tailspintopics.blogspot.com/2012/12/f-4s-wing.html
As it happened, according to Jan Jabobs, the first 43 F-4S conversions were completed without the maneuver slat modification that involved new outboard wing panels. These Phantoms were delivered to Marine Corps squadrons. Note that it does have the strip formation lights on the vertical fin and fuselage that were one of the external changes for the S configuration.
Photo by Toshiki Kudo at Kadena, 12 September 1981
At least one slat-less VMFA-251 F-4S had a suitable designation on the aft fuselage above the Bureau Number.
Photo by Rick Morgan at Key West, 7 December 1980
The slat-less Ss were subsequently modified to the full S configuration shown here. Note the much shorter ECM antenna fairing on the engine inlet than present on the F-4N, another characteristic of the J/S. (Rick pointed out the cool way the squadron's crusader sword outlined the F-4S formation light on the vertical fin.)
Photo by Rick Morgan at Key West, 3 August 1980At least a few F-4Ss with the slat modification also had the inboard leading edge flat reactivated. It was subsequently locked back up again.
I haven't addressed the various cockpit changes over time and don't intend to with the exception of the ejection seats. The first F-4s had the McDonnell-furnished ejection seat (an illustration is provided in one of those F-4A blogs referenced above) but it was soon replaced by the introduction of the Martin-Baker seat in almost all the Navy's fighters. (For more detail on the F4H seat change, see http://phantomphacts.blogspot.fr/2013/10/f4h-phantom-ii-ejection-seat-history.html.) The Mk 5 was installed in the Bs and the first Js. According to the June 1968 issue of Naval Aviation News, F-4Js began to be delivered with the Mk 7 in December 1967; the Mk 5s in the Bs and the earlier Js were modified to the Mk 7 configuration or replaced by Mk 7s. See http://thanlont.blogspot.com/2011/02/transition-to-martin-baker-ejection.html
*That letter that you sometimes see after the Bureau Number on Navy airplanes indicates the production block number, in this case "a" for Block 1. (BuNo 142259 was actually the very first Phantom; note that the designation is not YF4H-1 and "Navy" was still being included along with the designation and bureau number.)