Well, once we reach a certain point in our games, we have pretty dang big groundstrokes. Most rackets are in the SW1 category (the lower swingweights). Moving them up to SW2 status (high swingweights) adds control to our swings, as well as giving power and spin. No matter what, adding weight will pump up the swingweight (albeit to different levels based on WHERE you put it).
So basically, everyone that plays tennis on a high level and uses custom weighted rackets is eventually going to end up playing with ridiculously high swingweights (okay, ALMOST everyone; Verdasco is one of the exceptions). The difference is HOW they want to get there. Some people want rackets that are insanely stable and plow through the ball, giving insane amounts of power and control for anybody good enough to swing it around (like Sampras, Roddick, and Courier). Others like the rackets to be very easy to whip around, allowing them to use heavy amounts of wrist action in their shots and allowing them to generate unprecedented amounts of spin (like Rafter, Nadal and Federer).
To get insane amounts of stability and plow through on the ball, you need VERY high levels of mass on your racket so that you can barely feel the ball's "weight" on contact (you can still feel the ball extremely well, but you might notice a more muted response than before thanks to the added stability). But the more mass we add, the higher the swingweight. So if we do it wrong, we won't get as much mass as we want, and we'll already reach our ideal swingweight in the SW2 section. So these people will put the weights lower on their racket (closer to the center of the racket; 3&9, as well as around the throat or top of the grip for counterbalance). That way, they can put more weight on their rackets to reach the amount of power and plow through they want without exceeding their ideal swingweight specification. This is what we call a depolarized setup. It's what most pros used. 95% of pros (if not more) prior to the year 2000 used this kind of setup. A wood racket is essentially a depolarized racket, so 100% of people prior to graphite rackets used a depolarized setup.
Others like their rackets to be less hefty, while still having that nice, high swingweight. To do that, they want every bit of mass they add to increase the swingweight as much as possible, so that they add very little mass to the racket, but get that nice spike in swingweight. They will end up putting the weight near the top of the racket (under the bumper guard) and some inside the buttcap for counterbalance. But since at this point, people don't care too much about balance, most of the added weight goes under the bumper guard (I hear Nadal adds 9 grams under the bumper and 2 in the buttcap while all of Federer's added racket weight is under the bumper, which I'm guessing is 2.5-4.5 grams). These rackets have lower static weight and become more manageable and spin friendly. Also, since the weight is mainly distributed towards the ends of the rackets, it spins on it's axis better, allowing for even better access to spin and racket head speed. This is what we call a polarized setup. Nowadays, a lot more people are using this setup thanks to the lighter rackets out there. Also, this is the reason why we will see some pros with a ridiculously low racket mass.
Now, which setup is the best? That's up to personal preference, as stated before. I love both (currently using/trying a slightly polarized setup like Federer). A depolarized racket is the more conventional type of racket customization (as it's been around longer) but it's a little more difficult to do (overall, but it depends on the racket as well). It grants extra forgiveness, stability, and pop so most people should generally look to have this kind of setup. It's the best for aggressive baseline hitting, as well as for serve and volleying. If you want to take the ball on the rise, or are an aggressive returner (like Agassi and Blake; both of whom use a depolarized setup), then you'll love the stability and power this setup gives. The other one is better for people who feel like they have all the power, forgiveness, and stability they need, but are lacking in some spin and margin for their shots. This is where a polarized setup can help, because it really adds a lot of spin to your shots and gives you extra margin over the net to safely stay in points. Nadal uses this setup to great effectiveness, employing heavy spin off the forehand and serve, constantly pulling his opponents wide and out of position. Rafter liked it because his big weapon was his kick serve and athleticism. A polarized setup added extra kick and action to his serves. He would kick a high one up to the opponent's backhand, then use his athleticism and feel for the ball to put away volleys. Though, this caused him to be less effective on grass, where serve and volleyers should dominate (as you can guess, almost all serve and volleyers use a depolarized setup). However, I must say that I found the polarized setup to be more erratic overall. It becomes difficult to control the racket sometimes (because the power and spin might not always be as consistent due to lack of stability), but most of the time you'll get good results if you like to use heavy spin.