Well, a fader is a great thing - fading tracks in and out is a huge part of DJing. Also, try cutting - pop the fader back and forth quickly to give that chopped up effect like a vinyl DJ would. There are also stop record effects that you can use that sound like a record slowing to a stop. All those tried and true methods will work in the digital world.

Further, abuse your effects. Cut the track out with a big echo or delay if you bring it out at a lull in the next track - breakdown. Whatever you do, leave the flanger at home...lol.
Hope this helps.

use delay,reverb, or a combination of both on the end of the sample to help mask the sound of an abrupt cut. Ecspecially handy if the samples are noisy and very obvious when they come in and out.