There isn't an official policy. However, many gms have a policy of swapping out one known spell from the standard list for each spell gained from a non-standard list.
I myself take a slightly different take. Since I have many of the third party sources I have allocated them to the various races and countries.
First I created a list of common spells that everyone, regardless of race or nationality has access to. They are called core spells and here is the list for the 1st level cleric spells
1st Level
Bless
Bless/Curse Water
Cause Fear
Cure Light Wounds
Detect C/L/E/G
Endure Elements
Inflict Light Wounds
Protection From Alignment
Remove Fear
Sanctuary
The rest of the spells are secondary spells and can be gotten very easily with buying scrolls, spending downtime in school etc.
Spells from the Complete Series and other third party are harder to get.
First they are broken up by race and nation. For example, only the natives of Mu Tulan have access to spells from Relics and Rituals, only the Elves have access to spells from Oriental adventures, and only the Dwarves have access to the spells from magic of fearun. Some smaller books (like the enviromental series) are only available in a specific region or npc race.
If your character is from one of those groups then those spells are considered secondary spells. Otherwise they are considered tertieary spells. Study times are much longer; you can spend a feat to learn *one* if you have been exposed to it; you can trade or outright buy it, but prices are outrageously higher for outsiders. In some cases, the spells are considered state secrets and providing them to outsiders is treason.
Some players like to kill wizards and take thier spellbooks. I have no idea where they got that from.
