The system reference document (also known as the SRD) is a subset of the core rules of the Dungeons and Dragons Third Edition system (also known as the d20 System) that are free to be used by any third party publisher. This is one the strengths of the d20 system, you are free to build upon it like a piece of Open Source Software. (Also, you are required to give some amount of your new material back to the "Open Community" and make 15% of your document available for others to use.) The SRD does not contain everything that exists within the Core Rules (the Players Handbook, the Dungeon Masters Guide, and the Monster Manual) of D&D. For those things which are not part of the SRD, you are forbidden to mention them. (Such as character creation and how to "level up" a character.) This is the way that Wizards of the Coast allows for third parties to publish material for Dungeons and Dragons without giving up control of the game. (It also allows for items to be published which would be unprofitable for WotC, but which a smaller publisher would have a thriving business around.) Note, that the SRD is part of the Open Gaming License as well as the d20 License. (The d20 license is more stringent.)
If you are a d20 publisher and you are looking for what you are allowed to use, your best bet is to completely ignore the Core Rules and use only the SRD as your reference. There are other small tidbits of info which do not exist in the SRD, such as the info on some of the trademark D&D monsters (such as the displacer beast), some classic D&D magical items (such as the Sword of Kas), the deities (such as Vecna). Some things also changed name, the magic item Heward's Handy Haversack becomes "Handy Haversack." The spell "Tenser's Floating Disk" becomes "Floating Disk." This actually causes havok for some people, as the spells are alphabetized in a different fashion now. When you look up information for "Floating Disk" you need to know to look up under "T" for "Tenser's Floating Disk." Some publishers got around this by publishing their own list of spells with equivalent stats and information, but with new names. "Tens' Floating Disk" and such.
The SRD is a continually changing entity, so third party publishers might use a version of the SRD which later changes. There was a product on the market which was the "Guide to Illithids," but Wizards of the Coast later decided that the name Illithid was only available for their use and so third party publishers needed to use the name Mind Flayers. Luckily, most of the third party publishers are agile enough to adapt to these quick changes and Wizards is gracious enough to forgive any but a blatant disregard for the spirit of the rules. Still, it's best as a publisher to continually check the SRD when you design your material to make sure you work with the latest copy.