Via Make Better Media is the fun Star Trek transporter effect, below, from Videopedia. There's some interesting tidbits of info and a quick peek of another version effect in the new movie.
Among a variety of other things like The 24p Conspiracy, Videopedia has specific short Trek transporter tutorials for those who need them in Sony Vegas, Final Cut Pro, Adobe After Effects, Adobe Premiere, and for Traveling Mattes and Masks. Videopedia even gives you a particle clip for free, if you can't imagine ever using the built-in Particle World filter again.
Update: another style is from After Effect Tutorial StarTrek by Robin Cranson,