What do you consider when setting crossover freqs?

One problem is that the bass measurement changes when you change seats. If you are closer to a wall or corner, you will measure, hear, and feel more bass. You get it all figured out, but then move to the other end of the couch, and you might feel like you need to make adjustments. I think that is why people get more than one sub- it helps even things out a little bit. But then you have to balance your mains and 2 subs. AAAAAAAH! Just make sure you sit in the same place.

For Bass, set it by ear. In my unusual system where the custom subwoofers are good to 350 or so and the mains are MG1.6, good to 40 Hz, the best setting depends on the music. I have a convenient way to change the frequency (a knob).

usually 10hz below the main bottom response so the blending does not leave a bass hump - start low and move up til you hear it and then back down a notch, is a very basic STARTING point

when all else fails try the two pink things then engage grey matter follow with bubbly

Lot's of good theories here, including Chadlinz's input. It depends, though. In a perfect acoustic space and setup, you could find the 3db down point of the mains, and ajust the sub to mate. However there are other variables.
A main variable is that typical receiver and passive speaker combo's opperate much more efficiently - regardless of response potential of the mains - crossed over to a powered subwoofer at a certain frequency range. THX finds that at about 80hz. Set up well, I find that a superb location, personally.
Basically, even if your mains can play down to, say, 45 hz, I know from experience that you can get my better dynamics, dynamic range and power handling if you cross em over at 80hz, and let the active sub woofer handle the dirty dubties. The receiver (being week on current, relative to separates amps) needs all the dynamic help it can! Also, the typical medium sensitivity passive speaker also needs much dynamic help, as it can't control the drivers half as efficiently as an active configuration.
Another consideration, as hinted at here above by others, is that the room is a huge factor. You might find, for instance, that the best location - all factors considered - for the speakers might be where they have a down point, or even hole at a certain frequency, where they'd function better crossed over elsewhere. So it depends. Same can be said about the subwoofer, which needs care in placement.
So, it's a balancing act, with lots of variables to consider. Basically, there's no "this is THE BEST setting, er whatever, across the board.
Hope this helps