The following text is at the beginning of each errata file. (This one from the Player's Handbook errata.)
Errata Rule: Primary Sources
When you find a disagreement between two... rules sources, unless an official errata file says otherwise, the primary source is correct. One example of a primary/secondary source is text taking precedence over a table entry. An individual spell description takes precedence when the short description in the beginning of the spells chapter disagrees.
Another example of primary vs. secondary sources involves book and topic precedence. The Player's Handbook, for example, gives all the rules for playing the game, for playing PC races, and for using base class descriptions. If you find something on one of those
topics from the Dungeon Master's Guide or the Monster Manual that disagrees with the Player's Handbook, you should assume the Player's Handbook is the primary source. The Dungeon Master's Guide is the primary source for topics such as magic item descriptions, special material construction rules, and so on. The Monster Manual is the primary source for monster descriptions, templates, and supernatural, extraordinary, and spell-like abilities.
Many read this as saying that other texts are primary sources—for example, the Expanded Psionics Handbook as the primary source for psionics (replacing the earlier edition's Psionics Handbook as the primary source for psionics) and Tome of Battle: The Book of 9 Swords as the primary source for martial adepts and martial disciplines—, but the Errata Rule mentions no texts beyond the Player's Handbook, Dungeon Master's Guide, and Monster Manual. DMs must decide which sources beyond these (if any) are the primary sources for their campaigns.
But, clearly, the three core books take precedence over everything each covers, including the Player's Handbook's exceedingly broad mandate to cover "rules for playing the game" (whatever that means). (Note that the Player's Handbook and Dungeon Master's Guide are given non-exhaustive lists, but the Monster Manual is given what's apparently an exhaustive list, taking precedence only with regards those items. This is weird and probably not a huge source of worry to anyone unless one's going to gamer court.)
In one question, the D&D Frequently Asked Questions, Version 3.5 (last updated June 30, 2008) answers not an actual rules question but a publication question. That question is reproduced below:
Both [Complete Arcane] and [Player's Guide to Faerûn] include a feat named Innate Spell, but the prerequisites and uses per day differ. Which version is correct?
Unless stated otherwise, any time that a rule appears in two different sourcebooks (other than the PH, DMG, and MM), the most current sourcebook is considered correct and all previous sources are superseded. A book’s credits page lists its publication date (typically near the bottom of the page).
In this case, [Complete Arcane] (published in November 2004) supersedes [Player's Guide to Faerûn] (published in March 2004), and thus its version of Innate Spell should be considered the official version. (41-2)
I can't find another reference for this oft-quoted meta-rule.
In rare cases, this creates confusion. For example, the armor special ability fearsome that originally appeared in the Magic Item Compendium (Mar. 2007) was superseded by the much better armor special ability of the same name in Drow of the Underdark (May 2007) then was superseded again by the original version in the Magic Item Compendium (July 2013).1
Warning: There are Internet places where bringing the Main FAQ into a discussion gets one mocked, shouted down, and accused of witchcraft. It is cited here only out of necessity, and I will happily edit this answer to reflect rules provided by a more well-regarded source if one can be found.
- Which version of the armor special ability fearsome should be used in the campaign? Whatever the DM decides. This DM allows the version from Drow of the Underdark.
Seriously, and according to its own texts, Wizards of the Coast says
The Rules Compedium Can't Change the Core Rules
I know it's weird. I know it sounds like nonsense. I know that when the core rules were published things like swift actions didn't exist. I have shed blood on the Internet battlefield between the Rules Compendium declaring free actions are only available on one's turn versus the Player's Handbook slightly vague addressing of the topic, especially in conjunction with immediate actions. I know. I know.
Wizards of the Coast Created a Flawed Paradigm
Here's the skinny: All of the errata documents have this Errata Rule describing Primary Sources
Emphasis mine. So the most recent publication of the core rules--the 2013 editions of the Player's Handbook, Dungeon Master's Guide, and Monster Manual--are absolutely primary, even if topics within those texts were subtly changed, outright contradicted, or the subject of FAQ or game designer commentary by other texts between 2000 and 2013 before those texts' publications, and even if uncorrected errors remain in any of the most recently published core books that were corrected by other books before the core rule' republication.
Flaws other books set right may have been backwardly-uncorrected--or whatever Orwellian phrase you might want to use--by the republished core rules.
The Rules Compendium Asserts Its Own Primacy
The Rules Compendium's Introduction says
So while the Rules Compendium is meant to take precedence, it, officially, can't.
Why Reject the Rules Compendium?
Some folks enjoy playing by the rules--the rules are there, someone was paid to write them, and some (probably) paid to acquire them--, and having the core rules changed by a source and only that source makes them uncomfortable, like somebody's trying to pull a fast one. Some of the Rules Compendium's so-called clarifications are outright changes to the rules, and that bugs folks.
Examples of changes implemented by the Rules Compendium include...
"This is Bizarre! Can I read more?"
Sure. Giant in the Playground forums' Curmudgeon is probably the most articulate and vociferous proponent of the Rules Compendium's flawed existence. His comments here summarize his stance well, and it's a good read.
Note: I'd like to make this answer a repository of links to questions and answers that demonstrate where the core rules and RC differ. You can add such into the Examples of changes... yourself or leave a Comment.