If you get a chance, the Deadlands d20 setting has a very simple and very smart way to do spell points that I think is rather worth checking out. I'm not sure how much I can describe it here without breaking copywrite, especially since it basically has like 3 rules, but taking that system and applying it directly to D&D (minus the skill checks for casting) has a lot of potential.
One problem I've come across in creating spell point systems (and something to keep an eye out for in evaluating other systems) is that a direct cost -> point system can never work. Giving a wizard the ability to choose what spell he wants to cast when AND allowing him to cast 9 level 9 spells in a row (by using all of the spell points from all of his lower-level spells) is broken. Spell points need to give a caster fewer total casts for powerful spells in exchange for greater total cast potentials for lower level spells - however, they still need to be limited in how much casting they can do all at once. The Unearthed Arcana book tries to solve this problem by introducing the idea that all spells need more points in order to increase their effect; i.e. a fireball doesn't become 10d6 just because you're a level 20 wizard, you have to increase the spell cost for that spell. I personally don't like this idea, but it is one solution. Personally, I find very little problem in allowing a level 20 wizard to cast 50 magic missles a day, because they're essentially wasting their time - in the time it takes them to cast 50 missles, a comparable wizard could have wiped the floor with a couple meteors and been done with it.
Another big problem is that most spell point systems are overly complex or hard to implement. If you find a system using an elaborate chart that couldn't be summed up in a simple sentence (i.e. the highest level spell you can cast is your caster level divided by two, rounded down = a good and simple rule that is easy to follow), it isn't worth it. I've seen systems that were really good at capturing the essence of spell points that were worthless in a real game because it required too many charts and too much math.
To me, a good spell point system will take other factors into account when determining the amount of spell points; effective spontanious casting is a huge bonus to wizards and devine casters. I also like the idea of having fewer potential spells in just one setting, but allowing spell points to regen at a decent - but not enormous - rate (sounds like a good time to start enforcing those random monster rolls, hmm?). Sure, you can spend an hour to get back enough points to cast one more high level spell, but what if we run into another wandering band of whatevers? And lastly, the system really needs to be simple. If you get more than just a few rules, or elaborate charts - you need to rethink what you're doing.