Before you read on, a caveat: this does not apply to Vancian spellcasting. Spells should be powerful and rare, and I have other changes in place to reflect this.
I've been bandying about the idea of changing the mechanics of any class ability that is based on "daily uses".
Basically, any ability that is called out as 1/day in the class description is instead "At-will".
In cases where the ability has a duration, the maximum time it can be maintained varies, but after exceeding the maximum time Constitution checks are needed to maintain the effect. Abilities with durations cannot be activated when fatigued.
Finally, this borrows the concept of a "short rest". This is 1 hour of low-impact activity (no combat or spellcasting).
Barbarian - Rage: Maximum duration is 1 minute. Must have a short rest to recover.
Bard - Bardic Music: No other changes, the bard is already using actions to maintain the ability. Maximum duration is 1 hour (not perfect, but easy to remember). No rest to recover unless fatigued.
Cleric - Turn/Rebuke Undead: Each time the ability is used, effective cleric level is reduced by 1 (only for turn checks) until a short rest.
Druid - Wild Shape: X/day indicates how many forms the druid knows. Can change between those forms and normal form any number of times, unlimited duration.
Monk - Stunning Fist: Each time ability is used, reduce effective character level by 1 (before dividing by half) to determine save DC, until a short rest.
Paladin - Smite Evil: Standard attack to use. If the paladin smites an opponent that is not evil, they lose this ability until they can take a short rest (to pray).
Any Other Ability: Reduce effective level by 1 until a short rest.
Some abilities (like a ninja's invisibility are not appropriate for this system. For example, in that case, it is probably best to simply give ninjas a lesser form of Hide in Plain Sight at 1st level.
The immediate implications of this are that Sorcerers and Wizards are going to be worse off at low levels, and Fighters and other classes that don't rely on any sort of daily mechanic at all will be much worse off in general. As a fix, I would give Fighters and Rogues something to compensate for this, as well as giving Sorcerers and Wizards the ability to use cantrips at will, for a very minor power boost.
Other than than, for the most part this is a very elegant and nice idea. However, I'm a bit leery about Wild Shape. It's a very strong ability and even with the number of forms limited to a handful the versatility of a Druid who has unlimited use of that ability make it potentially very dangerous.