First thing, determine your system's priorities. Will you watch movies or listen to music? Most folks do one or the other.
Since more home theater speaker buyers watch movies than listen to music, I'll start there.
It's hardly an overstatement to claim movie-oriented home theater systems succeed or fail based on their center channel's performance and sound quality. The center speaker delivers virtually all the dialog and it can, depending on the mix, convey upward of 80 percent of a movie's soundtrack. The center speaker has a big job.
So invest 30 percent of your 5.1, 6.1, or 7.1 system budget on the center speaker, the Center Centric HT approach. As always, when it comes to sound quality, size matters. Bigger centers tend to sound better than small ones.
The subwoofer is the next most important player in a home theater sound system. Invest the next 30 percent of your dollars on the sub. The sub is largely responsible for home theater impact and power.
That leaves 40 percent of the budget for the front and surround left and right speakers. Of that, I'd put more bucks into the front speakers than the surrounds.
What I'm describing here is a little unconventional, but it's predicated on the belief that the best possible sounding center and sub are crucial for home theater performance. I'm also assuming all the speakers and probably the sub are from the same manufacturer.
For more music oriented home theaters the priorities are reversed. Fifty percent or more of the budget goes for the front left and right speakers, which should be large enough to produce bass without the aid of a subwoofer. The remaining budget is spent on the center and surround speakers (more on the center than surrounds). It's the "Stereo Plus Three HT" approach.
After all, music is mostly stereo, so it makes sense to put the lion's share of your dollars where they'll do the most good: The left and right front speakers.
Lastly, the 50/50 movies and music system. Evenly distribute your budget and buy the more typical "matched" system. Thing is, it won't sound as good as either the movie or music systems described above, when doing what they were designed to do.
I make my living writing about audio and reviewing tons of gear every year. My opinions about speaker sound quality are covered in the reviews. Asking advice from me or anybody else about speaker sound quality is like asking what's better, chocolate or strawberry? There's no definitive answer, it's a matter of taste.
With speakers and subs you really have to listen for yourself. That, or buy the ones I like the most.
7/19/09 Update: I'm happy to see some Audiophiliac readers have brought up the concept of stereo home theater, which works equally well for music and movies. I've been writing about HT 2.0 for years, and blogged about it last on April 4, 2008. HT 2.0 is an alternative approach, ideal for small bedroom, den or office systems. More speakers are just more speakers, but better speakers sound better. It's really as simple as that.