Common Magic (3.5e Variant Rule)

Common Magic
Even at low-levels, cantrips are not particularly potent spells, and by mid-level, most are either useless or superseded by skills or other spells. This rule tries to adjust for that by improving how these spells can be used, especially since some have some fairly practical utilitarian uses, but the players are restricted to a pitiful number of uses per day. Included is a work in progress idea for how non-spellcasters might be able to gain access to these weak spells, hereafter referred to as cantrips.

Normal Casters
For Wizards, Sorcerers, Clerics, Bards, Druids, and similar classes with existing access to cantrips, the rule is that cantrips known can be used at will. For spontaneous spellcasters, like sorcerers and dragons, the normal limit of cantrips known still applies, and no further changes need to be made save that those cantrips are usable at will, rather than 6/day total. For preparation spellcasters, the number of cantrip spell slots instead becomes the list of cantrips prepared for the day, each usable as often as the caster wants. For example, a first level wizard can prepare three cantrips (he chooses mage hand, dancing lights, and ghost sound), which he can use as often as he likes, but his first level spells remain unchanged (he, unlike a sorcerer, can change which cantrips he wants the next day). Caster levels and save DCs for cantrips remain tied to the class from which a character gets them (so arcane cantrips still have spell failure chance in armor, divine spells require any focus, etc.).

Cantrips can only be used at will if they are in a cantrip slot; using higher-level spell slots for additional cantrips does not allow them to be used at will (and again, why would you bother with that anyway).

If a class has access to a spell considered to be a cantrip for another class, but not for their class, it is treated as the higher spell level (not usable at will). An example would be the read magic spell, which is a cantrip for wizards, druids, clerics, and sorcerers, but a 1st level spell for rangers or paladins. If a ranger chooses to prepare read magic, she cannot use it at will. If a player can choose between two classes for such a spell, they are free to select the lower version for the class that grants it. Thus a cleric 2/paladin 7 multiclass character could prepare read magic as a cleric cantrip or as a 1st level paladin spell, whichever he desires.

Forbidden Cantrips (Variant Variant Rule)
Damaging and healing cantrips are a special case, which depending on the needs of the campaign could remain at-will abilities or be banned altogether. Most damaging cantrips are rarely powerful enough even at low-levels to be any more than a basic attack, and generally trade the advantage of using a touch AC for far less damage than even a basic weapon, like a sling. As characters advance in level, this becomes even less of an issue as more powerful spells become more pratical (many of which harm foes in non-hit point related ways). Under no circumstance should damaging cantrips be retained under the base D&D rules if other cantrips are to be used under this rule, since it is unlikely a player would take it, and it is simply easier to ban damaging cantrips altogether.

Cure/inflict minor wounds are a special case, in that these cantrips can be used to heal, as well as harm, foes. Again, in all but the lowest level settings, taking several minutes to heal party members is too slow to be easily abused, so provided players can act responsibly when using these spells, you could retain cure/inflict minor wounds with little bother. If not, simply ban the spells. Note that these are a separate category from damaging cantrips because they heal and damage, and as such both can be used, the cure/inflict cantrips can be banned, or all damaging cantrips may be banned. Since the objection to at-will damaging cantrips is partially the same as at-will healing cantrips, it makes little sense to ban damaging cantrips but not healing ones.

Metamagic
There seems to be very little point in applying metamagic feats to cantrips under the current rules (although I am open to the idea that there are good strategies), so I see no reason not to ban applying metamagic feats to cantrips. If you wish to continue that, just remember that it usually uses a higher-level spell slot (and the few that don't are damage/healing spells, which are forbidden in any case), so it no longer counts as a cantrip and is no longer usable at will. However, a spellcaster, such as a wizard, could prepare both the normal version of the cantrip and one or more with metamagic feats.

One exception are metamagic feats which do not change the spell level of the spell, such as the energy modification feats in Complete Arcane. It is perfectly acceptable to use cantrips with these feats.

Cantrips from Feats
A number of feats from 3.5e sourcebooks (and possibly earlier than that) include feats that grant spells or spell-like abilities, among which are cantrips. As it stands, these feats are rarely worth taking even at low-levels, and under these rules, their value as they are now written is even worse. While I recommend not taking these feats at all, if a character does take them, the normal at will limit applies to cantrips ONLY, not any other abilities granted unless noted otherwise in the feat description. For example, Complete Arcane has several feats that grant two 0th level cantrips, and one 1st level spell, as spell-like abilities; only the cantrips are at-will. Caster level for spell-like abilities is determined by existing spell-like abilities caster level, or the limits of the feat, whichever is higher, while unless a character has class levels in a class that normally grants that ability (minimum 1st level). NOte that because you use a feat to get these spell-like abilities, these do not count against any you learn through normal spell means or through the variant for non-casters described below.

Cantrips as Spell-like Abilities
Creatures which have non-forbidden cantrips as spell-like abilities may use them at will; this hardly alters their challenge rating enough to be an issue. Those that do possess a forbidden cantrip (if applicable) as a spell-like ability may either retain that ability to cast it, or have it replaced with one or more comparable and thematically appropriate equivalents.

Magic for Noncasters
Cantrips offer the chance to give non-casters and non-traditional casters some of the tricks a full caster receives, without diluting the power of either class. This is still a work-in-progress idea, but a non-caster who gains at least 3 each ranks in Spellcraft and Knowledge (arcana) for Sor/Wiz, Knowledge (nature) for Drd, and Knowledge (religion) for Clr (or Arcana/Geomancy/Thaumaturgy) for Tome of Prowess characters) may learn a number of cantrips equal to one-third their character level (minimum 1), in a fashion similar to a sorcerer (usually requiring an instructor who already knows spellcasting). Characters can learn any combination of cantrips they can master, but with a few caveats. They must use the key ability score for that attribute to cast the spell (varies by system and by class), and their CL is 1st, unless they have access to spell-like abilities from another source, in which case that caster level trumps the base one. If they ever take levels in a class from which they learn cantrips, those they know are part of, not in addition to, those cantrips they gain through the class.