Well, "best" could mean a lot of different things in different situations.
For THE BEST low degree cooling of your CPU, you could use Liquid Nitrogen. But, as you can surmise, Liquid Nitrogen is probably not the best cooling system for most people as the explosive aspect of this solution.
Then there's the ProMetia cooling system, that runs similar to an A/C or Refrigeration unit. That method will give below zero degree temperatures, and is relatively safe and once it's set, you don't have to fiddle with it much. Although it does cost upwards of $600. So, there's another possibility for the "Best" but then again, maybe it's not the "best".
See what I mean?? The "BEST" solution, depends on the situation.
There's peltier cooling(this is what you were thinking), where one side of a plate cools the CPU, while the other gets hot. Well, this one will cool fine, but normally you need water cooling, just to be able to cool the peltier plate down to respectable temps. (Vicious cycle, eh?)
Water cooling is the most widely used cooling solution besides Air cooling, and while it is almost silent(most of the time) and can offer quite a bit better temps thatn Air cooling, there is also more work involved, and if you were building a system to sell to a friend/client, you might have more trouble doing so with a water cooled system, than with an air cooled one.
Then there's the good ole' heatsink and fan(which in my mind is STILL the "best" overall). They are just so versatile. You can use them in big systems, little systems. There's really not much mess to putting them toogether. (four screws ain't THAT hard to screw in!)
PLUS, all you have to do is plug them in, and the fan starts turning. Voila! You have a CPU cooler. THe hardest part about them is getting the bracket snapped onto the CPU holder. (Many will attest to this.) But, for that little bit of trouble you have a reliable cooler. No it's not the "best" for cooling, No it's not the "best" for noise, No it's not the "best" performance cooler, No it's not the "best" at turning heads, but to me, it's the "best" in that it's inexpensive, easily replaceable, simple diagnostics(if the fan's turning, it works, if the fan is not moving, it's broke), ease of installation, peace of mind(you can normally hear it to know that it's on), less maintenance(just clean off dust peridoically), no cutting hose/pipe, not modding your case to fit it inside, many different styles/types available, and did I mention cheap??
So, all in all, I guess it depends on how you define the word "best"...
David