With strats it depends on what type of tone you're after. I love strats so here we go:
You've got Alnico 2 magnets and Alnico 5 generally to choose from. The Alnico 2 magnets are slightly weaker, but the pickup itself is often wound hotter then most singles that use Alnico 5 magnets. As a result you get a woolier mid-range type of tone, still a single coil, but with a little more punch.
The traditional strat single is usually an underwound pickup with Alnico 5 magnets. Lately companies are winding their strat pickups hotter, vintage strat pickups are usually somewhere between 5-6.5k, now the average strat pickup is probably closer to a 6-7.5k. There is a misconception among consumers that hotter pickups will sound more like SRV or Hendrix, or some other strat slinger, when in reality they all used vintage spec pickups in their strats which were usually underwound. They got their hot tone by turning the amp up and heating up the tubes more, not by having hotter pickups.
For me, the best strat tone is a relatively weak pickup with a slight dip in the mid-range, as opposed to a boost in the midrange. Texas Specials sound alright, but they do have more mid-range and output then is typical of original strats.
I've never liked Dimarzio's strat pickups. Seymour Duncan makes a better strat pickup, if you have the money go for the Antiquity IIs, they're underwound Alnico 5s. But if you want the hotter tone he does have the Antiquity I which is a hotter Alnico 2. If you don't have the money his SSl 1s will get you in the ballpark of the vintage tone of the Antiquity IIs, and the SSl6 will get you the hotter tone. He also has the SSl52s, which use Alnico 2 magnets on the high strings to mellow them out, and Alnico 5 magnets on the low strings to brighten them up, this gives a very nice round balanced tone.
Now if you really want great strat tone, there are the boutique guys. Van Zandt, Lollar, Lindy Fralin, and Voodoo Pickups. All these guys have their versions of high and low output strat pickups. I've tried the Van Zandt Blues pickups and they sounded great. I've also played a strat that had custom underwound Voodoo Pickups in them, it also sounded great and had terrific tone and response to pick attack. One of my past teachers had a very Eric Johnson like tone with his Lindy Fralin pickups. As of right now I've only got one strat and it is equipped with Seymour Duncan Antiquity IIs at the neck and middle and a Custom output bridge pickup wound by the Seymour Duncan custom shop that sounds somewhat like a tele bridge pickup.
The coolest strat pickups I've actually heard and played around on a few times are the Big Dippers made by Fender that can only be found on the John Mayer Signature Strat, but they do show up on ebay sometimes. They are "Big Dippers" because there is even less mid-range in these pickups then is typical of strat pickups. This combined with a slightly cranked tube amp, and a TS type pedal (which will boost the mid-range) is great for a nice even vocal tone from these pickups.
Some basic guidelines for strat pickups are to put two closely matched Alnico 5 pickups at the neck and middle (with the middle being Reverse wound polarity for hum cancelling in certain positions), combined with a hotter Alnico 2 or Alnico 5 pickup at the bridge. You want to set the bridge pickup height first with the end facing the high strings slightly higher then the end facing the low stings. Raise it until it sounds bright but not harsh, then raise your middle position pickup until you have the maximum amount of quack in position 4 (bridge and middle combined), now raise the neck pickup until you have the optimum amount of quack in position 2 (neck and middle). This should ensure balance and clear clean tone between all the positions.
Hope that helps!
Oh and if you're building a strat, make sure to use a nice piece of alder or ash, and if possible finish it in Nitro instead of Poly, you'll be much happier with the look, weight, and tone of the guitar that way.
