I haven't seen anything to this effect generically in 3.X; limitations like that would tend to be setting specific, and I don't recall any examples.
I've never seen anything like this so I just go with where the spell comes from. Under 3.5 which we're still playing until PF comes out, my general rule of thumb is this.
- PHB = common
- Spell Compendium = uncommon
- PHB2 = uncommon
- All/most other splat books = rare
I believe that you could consider anything in the PRPG Core Rules / PHB as "Common" for all practical purposes.
The spells that are specific to a given 'popular' clerical or wide spread society would be "Uncommon" while those specific to a magical college/academy, core class (Paladin-only spells, the spells in PHB 2 that appear on the Beguiler's class list that can also 'port' over to other classes) or specific modules would probably be "Rare".
"Very Rare" should be spells unique to a specific spell caster, "ancient" spells and spells from a region that is exotic to where a character is normally located.
I like considering various spells to be more or less easily available. A general rule of thumb, of course, is that the fewer people that know a spell, the fewer opportunities there will be to learn it. Some tags, which stack:
The higher the level it is, the fewer casters will know it -- going off of the price progressions, the number of casters in the world that know level X spells seems to go down by factors of 1/X^2. They will also be peerier about letting study materials for it get around.
Any spell which is strictly for a low-casting class, such as paladin or ranger, will be vanishingly rare.
An alignment descriptor will cut a spell's audience by about half.
Any spell with obvious criminal uses will be less available in an orderly society; weapons will be circumscribed by law ("Sir, we note that you've failed to attend annual safety training for your ice storm spell; you're fined 100 gold and ordered to attend training within two weeks.") at a level you'd like the society to practice its 'gun control', while healer and crafting magics will be more readily available. Obviously anything involving evil powers, death magic, or the like will have attempts to learn it noticed.
Spells with obvious governmental uses, such as Zone of Truth, on the other hand, may be widely available.
For somthing like this I think it's better for it to really be setting specific (or at least your own version of the setting in the case of pre-written ones, such as Golarian).
If you want certain spells to be more common, make it so. Make most NPC's learn them and encourage the players to think of reasons why they use the spells they use instead of simply taking them.
I think the best way to implement such would be to have organisations require certain spells. An organization dedicated to healing, for instance, might not allow members unless they know various healing spells (or at the very least, higher ups would need access to the spells).
If theres a magic organization dedicated to defending a city, have the group only include mages that can use spells such as Wind Wall (to deflect arrow vollies), stone shape (to alter/repair palisades) etc. Or even have the group split into several sections (such as offensive mages, diviners to detect battle plans and relay infomation, a group dedicated to setting up the battlefield via magical traps and crafting magical items etc) with each section required to learn it's own spells. This means that should the party say...for instance, find themselves fighting the offensive mages, each mage will likely have access to a similer (if not the same) spell list.
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The house rule I have recently begun to enforce when I DM, is that only PHB spells are normally accessable. When I say normally accessable, I mean when a Wizard gets new spells for leveling up, what a Cleric or Sorcerer can freely pick from. I do allow Domains (usually only one) from the Spell Compendium, but that is more to diversify Clerics. Some classes, like Warmage, still get their normal full spell list, but only a Cleric can train another Cleric, a Wizard another Wizard, so a Wizard couldn't go to a Warmage to learn a spell, even if they can both cast it.
There are only two ways really, to recieve other spells. One is through individual research, which has a Rping aspect to it, but is otherwise like in the DMG. The other, is to in game, actually find a teacher, a scroll, a spell book, or something like that, and actually spend time learning it. Followed by a Class Level + Spell Stat check against a DC 15+ Spell Level, modified by the amount of time and effort they put into it.
I like it that it allows me, as DM, to manage what abilities they have access to. I'm not overly strict, but the more potential that a spell has to be broken, the more difficult it is to gain. That way, at the very least, the caster understands that they really did have to earn what they abuse. So far, and i don't have a lot of experience with it yet, it does cut back on the powergaming some.