The version often shown on Sci-Fi is the longer unauthorized cut.
I believe the Lynch version captures the tone and feeling of the book much better than the new versions, and, when you get right down to it, the movie simply looks better. Its like comparing DYRL to SDF Macross. The sets, effects, and costumes for the new version looked like your stardard low budget made for TV cheesy sci-fi movie.
Of course, this isn't even taking into account the superior cast of the movie.