Personally, if I'm changing between incompatible types of brake fluid, I remove the calipers and rinse the inside behind the piston with Safety-Kleen, then set them where the SK will drip out and eventually evaporate, then I pump all the fluid through the lines until it's just air, fill up with the new stuff, and waste about a pint total pumping it through the lines before putting the calipers back on and wasting maybe another cup.
I don't know if this really is removing every vestige of the incompatible fluid, but I haven't had problems in the past and likely will never do this job again since I've standardized on DOT4 for everything.
When simply doing a flush/replace, I do pretty much the same thing but leave the calipers on, pump all the fluid out of the system, then fill it back up with the new stuff and bleed the system normally.
Of course, when doing this, it's important to bleed the master cylinder first, though this can usually be avoided by just not letting it get completely empty. I'm a little (okay, a lot) anal about brakes, though, and don't like to take a chance on any of the old fluid getting mixed with the new.
For the kind of use my cars see, they prefer that we do a complete brake fluid change every 6 months, but just like with motor oil, I do it based on how the fluid looks. If I can easily see the level because it's not very colorless anymore, I'll do just a partial flush, pumping enough through that I see fresh fluid at the calipers. The whole emptying/refilling is done at the beginning of every season.
A vacuum bleeder is indispensible, but I'm sure I'll soon get a pressurizer that attaches to the master cylinder.
