Hello,
The parts needing to be fitted to the hull surface are modeled by cutting out the portion of the hull surface where the greeble will sit. Then a basic block is extruded upwards at right angles to provide the starting shape to create the greeble.
For pipes, I use Lightwave's "spline draw" function by precisely placing points above the hull surface. The function then creates an accurately drawn spline curve defined by those points. Then I create a disc in another layer and position it at the end of the line. Finally, I use the "rail extrude" function to extrude the disc into a pipe defined by the path of the spline curve. The result is a perfectly fitted pipe.
Fitting a mesh to another mesh is far more difficult and time consuming, resulting in distortions of the original mesh. Some greebles are fitted manually in areas where the bends are very small and not noticeable.
[Edit] 12-24-10: 1 more greeble added today!
I hope all this helps. Cheers...