Well, I know one system that would work that, like Andy said, probably wouldn't be suitable because it would change things too much for some folks. We use this system in E.N. Publishing's The Elements of Magic, but it does shift away from the D&D standard quite a bit. I'm jury-rigging it a bit so you don't need EOM to actually use it.
Y'know how everyone has a base attack bonus, and BAB from different classes stack? Well, in this system, every magic-using class has a caster level bonus, and caster levels from different classes stack. Your caster level determines what power level of spells you can learn and cast, and how many spell slots you have.
Different classes have different lists of spells they can learn. Unlike clerics and druids, you don't gain access to all the spells from your spell list automatically. At at level you learn 6 cantrips and 4 1st level spells, and each level thereafter you learn any 4 spells from levels you can cast. The spells that you learn must be available on your class's spell list.
For example, you're a Cleric 2. You know 6 cleric cantrips and 8 cleric 1st level spells. Then you add a level of wizard, and since your caster level is 3, you can cast up to 2nd level spells. So you choose any 4 wizard spells from 0th to 2nd level, and you learn those. You'd have all the spell slots of a 3rd-level caster, and could use them for any spells you know. You could cast cleric spells in armor.
Obviously, this system would require a few changes, the least of which would be having just one table of spells per day. Also, you'd have a table that goes up by 1/2-levels, because some classes would only grant fractional caster level advancement. For instance, it'd be too powerful to go Cleric 19, then add a level of wizard for the 9th level attack spells, since you'd have Cleric hp, bab, and saves. Bards, clerics, and druids would have to have fractional caster level advancement.
For spontaneous spellcasters, it's kinda hard to fit them into the same rules as preparation-based casters, but not impossible. Whenever you prepare spells for the day, you can choose to leave slots open. These open slots can only be used for spells you know from a spontaneous-casting class.
Caster Level Advancement:
There are three rates of advancement for spellcasters.
Good. +1 caster level per level. Sorcerers and wizards.
Average. +3 caster level per 4 levels. Bards, clerics, druids.
Poor. +1 caster level per 2 levels. Paladins and rangers.
So let's imagine a hypothetical character, whom we'll call Merlin. He's a Bard 2/Cleric 2/Druid 7/Sorcerer 4/Wizard 5. His caster level is (8 from the bard, cleric, and druid levels, plus 9 from his sorcerer and wizard levels) a total of 17. He'd know a few spells from each class.
Like I said, a lot of little things would need to change, but I think it wouldn't be too hard for them to fit together. Then again, we decided that for The Elements of Magic we would more enjoy creating our own new spellcasting system that's even more flexible, and doesn't rely on standard D&D spellcasting archetypes. We let you make the type of caster you want, but I just wanted to show that the core rules could be made flexible pretty easily.
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