This article contains spoilers. Read at your own risk!
Since Half-Life's release, several retcons have been made to the series' canon. Most of them are minor, and were made by the team to accommodate the subsequent games' storylines. They do not affect gameplay and the main plot.
These retcons have been applied not only to Half-Life, but also to its sequels and spin-offs, as well as other canon sources, such as ApertureScience.com.
In Half-Life and its expansions, scientists and security guards are generic NPCs with only a few variations. Later, Valve and Gearbox based actual characters on the these NPC types, sometimes also reusing their nicknames as the new character's name:
The bald scientist model wearing thick framed glasses ("scientist01", or "Walter") was turned into the character Walter Bennet for Blue Shift. Later, for Half-Life 2, "Walter" was again turned in a character, this time into Isaac Kleiner. Although it is still unknown if he is seen in Half-Life as a real character, a scene in the game shows such a scientist wielding a shotgun, which mirrors a Half-Life 2 scene in which Kleiner does the same. Kleiner's name is also retconned: in old documents he is referred to as Alex, but in Half-Life 2 he is called Isaac.
The African-American scientist model ("scientist03", or "Luther") was turned into the character Eli Vance for Half-Life 2. Eli is said to have lived at the Black Mesa Research Facility with his wife and daughter, although they are not seen or mentioned in Half-Life. Eli was retconned in Half-Life as the African-American scientist sending Gordon for help right after the Resonance Cascade. In Black Mesa East, Eli tells Gordon after meeting him again: "The last time I saw you, I sent you up for help after the Resonance Cascade. I never thought it would take you this long to get back to me!".
The generic "Barney" security guard model was turned into Blue Shift’s main protagonist, Barney Calhoun, and was established as the security guard pounding on a door along Sector C Line at the very start of Half-Life, although Blue Shift retconned the fact that he already had his vest, helmet and flashlight. He was later brought back for Half-Life 2 and its episodes as one of the main protagonists.
The generic "Otis" security guard model was turned into the character Otis Laurey. However he is only mentioned in the Half-Life PlayStation 2 instruction manual, and whether he is seen in-game or not is unknown.
As seen in Kleiner's Lab in Half-Life 2, several members of Black Mesa's Anomalous Materials team posed for a photograph in the Anomalous Materials entrance hall, which was taken before the Black Mesa Incident, including scientists never seen before. It features Gordon Freeman, what appears to be Wallace Breen crossed out, three unknown scientists, and the four scientist models. As said above, two of them, "Walter", and "Luther", made their way into real characters. The two other models, "Einstein" and "Slick", seem to appear here as standalone characters, but this has not been developed yet. Out of the three unknown scientists, the man and the woman from the left appear on a Borealis image present in Judith Mossman's message.
Barney says at the beginning of Half-Life 2 that he owes Gordon a beer; this is a reference to one of the random sentences said by security guards in Half-Life. In Half-Life 2, it is implied that Barney actually said this at least once to Gordon back then, although Freeman never actually has a chance to converse with the retconned Barney in the original game.
In the Half-Life Audio Script, the Administrator evoked by the scientists is revealed to be the G-Man, suggesting he is the one overseeing experiments. For Half-Life 2, the G-Man was retconned as a more independent entity, and Wallace Breen was created to retroactively fill the Administrator's shoes.
The meal ruined in the microwave oven at the start of Half-Life was later said to belong to Arne Magnusson, although that does not prove that the scientist sitting on the table near the microwave oven is actually a retconned Magnusson or simply an unrelated scientist.
In the Opposing Force instruction manual, March is given as the month during which the Black Mesa Incident occurs, while it is given as May in other sources.
The timespan between Half-Life and Half-Life 2 was originally of 10 years, which was subsequently changed to roughly 20 years at the time of Episode One’s release.
While older sources state that Gordon only started work at Black Mesa the day before the incident,Half-Life 2 and Episode One make it clear that Gordon had been working at Black Mesa for some time before the incident, enough for Barney to owe him a beer, and to race against him in air ducts to open Kleiner's office whenever he locked himself out of it. Also, in Opposing Force, in the chapter "Crush Depth" A framed picture of Gordon is seen on the wall labeled "Employee of the Month".
Several changes made to the dates pertaining to Aperture Science originally given in the ApertureScience.com timeline were given by Game Informer in 2010 (they were written by Erik Wolpaw): "1978", the date for Cave Johnson's moon rock poisoning, was changed to "1974". "1979", the date for Johnson's kidney failure, was changed to "1976". "1975", the date when Aperture Science ceased to produce only shower curtains, was changed to "1973". The last paragraph of the timeline was also expanded, stating that GLaDOS was activated in 1998 instead of the original "Several Years Later", at that a few days later the Black Mesa Incident occurred, thus placing Half-Life during the same year as its release, while it was known as "200-" in every source (in-universe documents featured in the instruction manuals). It was however stated later by Marc Laidlaw that "1998" was incorrect and that 200-" was indeed the proper date. The original ApertureScience.com timeline was further altered in Portal 2.
The Combine being involved in the events of Half-Life. Even though some entity was behind the Nihilanth's actions, it was likely not defined as precisely as it is today.
The name "Vortigaunt" and parts of their culture (i.e. the concepts of Vortessence and the Vortigese language) were first formally introduced in Half-Life 2. In Half-Life, Vortigaunts were simply known as "Alien Slaves" (although the name is only mentioned in the Half-Life guide and Raising the Bar, and never in-game), even though the entity "monster_vortigaunt" already existed. The fact that the Vortigaunts turned from antagonists to protagonists in Half-Life 2 and its Episodes is not a retcon, but the results of Gordon's actions in Half-Life. Furthermore, the fact that the Vortigaunts were unwillingly antagonists during the Black Mesa Incident was also not introduced in Half-Life 2, as they are already known as slaves, and most of all are friendly and show peaceful communication with each other at the start of the Half-Life chapter Interloper. The Vortigese is also very different and more aggressive in Half-Life and its expansions, which was changed into a more gentle tone for Half-Life 2.
The Chumtoad and the yellow Boid were originally cut from Half-Life, and were brought back in Blue Shift. They are the only two cut enemies to have eventually made their way into canon.
The design of enemies like the Headcrab and the Barnacle are changed constantly on the franchise, depending mainly on the theme and the graphics engine of the game.
One entrance to Level 3 Dormitories, connected to the Transit System, is first seen in Half-Life, then seen again in Blue Shift. In Decay, the dorms are visited and are seen to feature two entrances, both connected to the Transit System. The entrance featured in Half-Life and Blue Shift is identified to be the north entrance, and appears to have been completely redesigned.
Half-Life: Source features several minor changes that could be considered as retcons. Of note is the Surface Tensioncanyon: along the cliff are located two large pipes that are supposed to extend to the root of the cliff below, but stop before, due to the game limitations of that time. In Half-Life: Source, they have been extended to the bottom and finally the river below, for more realism.
The Portal ending was changed (or rather, expanded) on a March 3, 2010 update of the game, having, instead of the original fadeout, Chell being dragged away by the Party Escort Bot saying "Thank you for assuming the party escort submission position". It was made to "re-energize" Portal and bridge the gap between it and its sequel Portal 2. The radios added in Portal in the March 1st, 2010 update are however likely non-canonical, as they only serve the ARG.
Portal 2 features several retcons, aesthetic and factual. As for the aesthetic aspects, some elements of the Enrichment Center featured in the first Portal have been redesigned (other than being in a state of disrepair), such as the Vital Apparatus Vent, Test Chamber 02's design, the elevators, the doors in the original Test Chambers, the corridors leading to GLaDOS' original chamber, or GLaDOS' design itself. As for the factual aspects, they mostly affect the history of Aperture Science, for instance the reason and era of Cave Johnson's poisoning.
At the end of Half-Life, G-Man lets Gordon keep his hazard suit. However, he awakens in Half-Life 2 without one and re-acquires it later in the game. It is unknown if this is a retcon, or if Kliener's possession of the suit is G-Man's doing.