I think switching pups and changing wiring schemes are two of the easiest and most dramatic changes you can do to change the tone. I have nine strats, each with different pups.....
1)57/62s - I really like these a lot. They retain a lot of the sparkle and chime but the neck has a nice bluesy tone.
2)Fralin SP43's - probably my favourites since I play louder stuff and these guys have that in spades. The bridge is in P-90 territory and gives you some real crunch when using a good tube amp. I think these are the best sounding strat pups I have. (currently)
3)Fralin Vintage Hots - another great sounding set of pups from Lindy. These have all the airyness (is that a word!??) and chime of the late 50's but also can overdrive a tube amp quite well. I love the tone from these guys when paired with a blender-type wiring scheme......very versatile.
4)Copperhead 1959 set - relatively unknown Canadian hand-wound pups which are very affordable and sound great. A little noisy since they are not RW but they retain a lot of the classic strat tones with some really nice dynamics. They really respond well to picking technique and are very height sensitive. I'm still tweaking mine everytime I play the strat that I have them in.........cool and well priced!
5)American Alnico II's = pretty good sounding pups in my VG strat. A little flatter and lower output than what I normally like but they sound good enough that I won't ever change them from this guitar.
6)Keystones - great sounding pups from the legends Bill and Becky. They sound really good and are again, very height sensitive. They only complaint I have is the neck tone; don't know if it's the output but it doesn't come across as meaty as others. The neck and middle are great though and I think the middle position is the best!
7)Fender CS Fat 50's - bought these because I had heard good things about them and they are very good. They have a really nice top end that shimmers. Think Eric Johnson clean; what they don't do so well is drive the tubes in my amp.

Seymour Duncan duckbuckers and Lil'59 - I really like SD pups and these things are very good sounding. For recording, I will often grab this strat because it is so silent. Also, the high output from the bridge really does give a great humbucker tone. I am always surprised and happy to hear how quiet and transparent these pups are.........they sound great with a tube amp but maybe even better in the digital realm with lots of effects.
9)Seymour Duncan JBjr and Texas Specials - I have one mongrel strat with a combo of these pups and they sound pretty good together. They bridge is very loud compared to the TS and even rolling off the volume doesn't really let you equalize the tone from all three. I am a fan of Texas Specials (even though they often get a bad rap) but the neck tone is very SRV and thick. Like them a lot.
So, there is my assessment from what I know. For me, the Fralin SP43's are the best sounding all-around pups for a strat but they are not cheap. Combined with blender wiring, they are amazing sounds pups!