There are tons of different magic systems out there. Unearthed Arcana has both spell points and recharge-time systems.
The Sovereign Stone setting used a casting threshold system where you rolled to build-up the power to cast the spell.
Arcana Evolved is vancian with more flexibility to heighten/Diminish spells.
EN pub's Elements of Magic (and EOM:Mythic Earth) are two more takes on the subject (and buying them helps support the site).
Green Ronin's Black Company and Thieves World settings have their own spellbuilding/casting system. Their True Sorcery is another.
Of course, the XPH psionics make a fine spell system with just a little (if any) re-skinning.
That's just what comes off the top of my head.
These are probably the most popular ones out there. My opinions from my kick-the-tires sessions:
Sovereign Stone
Pros: nice system, non-Vancian, spell creation rules. Spell roll to cast.
Cons: Little or no class differentiation for spellcasters. You can cast or you can't. (Going from memory here and it's been awhile but mechanically I don't recall significant differences.)
Elements of Magic
Pros: Very customizable, non-Vancian, easy to build magical "traditions" that focus on particular paths/forms of spells
Cons: Math-heavy. Build spells in advance or prepare for play to come to halt. Effectively, you are recreating the wheel in some cases in order to port your d20 spells to EoM.
True Sorcery
Pros: Customizable, including appendices for applying it to other d20/OGL games (e.g. applying True Sorcery to Thieves' World classes or Iron Heroes), non-Vancian, spell roll vs. drain. Versatile like EoM, but more codified for easier creation at the game table. We saw less of a slowdown than EoM.
Cons: Defining magical traditions is easy. However, if using D&D arcane/divine divide, you're probably going to experience a lot of overlap. Slowdown during play if spells aren't built in advance.
Arcana Evolved
Pros: Vancian-familiarity offset by increased flexibility (everyone casts like a Sorceror -- spell slots really just represent energy you have to cast). Unique spell classifications (simple, complex, exotic) & templates allows for custom paths/traditions. Spellcaster class differentiation. Spell Treasury does AE treatment of most SRD spells.
Cons: AE spells similar but not same as D&D spells. Vancian-modification effectively eliminates difference between Wizard & Sorceror. (You'd want to use AE's Magister anyway.)
Thieves' World
Pros: Non-vancian. Spell roll to cast. Drain (non-lethal damage) as caster limitation. Uses standard D20 spells. Supports arcane/divine divide. Differentiates between ritual and standard casting techniques (spells are the same but if cast as rituals have longer durations -- mages are better at spells; priests are better at rituals; witches are average at both)
Cons: Witch kills druid and takes his spell list.
My personal ranking:
#5. Elements of Magic - It's neat, I love the magical tradition-building component of it. Ultimately, it slowed down the game and was too much work. I couldnt' justify building spells when I had multiple sourcebooks with ready made spells on the shelf.
#4. Sovereign Stone - An inspiration for the TW system. However, the unique spells either had to be applied to classes or I had to convert D&D spells into the SS system. The spell-creation rules made it fairly easy to do, however. I just didn't want to spend the time.
#3. True Sorcery - Great system, very evocative of what you see in fantasy fiction. Would be in the top 2 if my players opted more for spellcasters than warriors.
#2. Thieves' World - Hit every objective I had. Can use standard spells while eliminating vancian spell slots. This is the system I use most frequently. Sexy, does what I need it to do, and is also the path of least resistance. So why isn't it #1...
#1. Arcana Evolved - More than any other D20 game, this one made me want to play a spellcaster. Not just any spellcaster (though the magister is my favorite) but ALL of the spellcasters. The most innovative treatment of the D&D style magic I've seen. Spell templates, Simple-Complex-Exotic spell divisions, Vancian spell slots I can stomach, laden spells, heightened spells, diminished spells. The Spell Treasury doing an AE treatment of the SRD spells was just a giant-sized cherry on top.