Exposed pipework and power conduit works quite well, as long as you run it in an organised way. Keep it to the edges and follow the contours of a build along walls, or hang it from the ceiling if you'd prefer a shorter route.
Machinery is a primary design feature- so make a feature out of them. Immersive engineering scaffold blocks work rather well for raising them off the floor. (makes them look bigger, and gives more height variation).
-does a machine take/produce liquid?
give it some big tanks from Railcraft.
As for the factory buildings
-solid fuel furnaces and smokestacks? The smoker block (Railcraft) can
really finish the look. And it responds to redstone control-
so a bit of sideshow magic [Buildcraft gates] and a blast furnace can belch out black smoke when its running.
-skylights in the roof, with the roof typically flat or with long, shallow corrugations. (I've never finished the roof- always another floor to add
)
-windows in the walls are optional- some factories don't, but those that do use either a lot of glass for as much natural lighting as possible- or have a row of windows higher up on the wall.
-avoid flat walls; add in some supporting pillars and crossbeams to support the machinery. Small details like support brackets go a long way.
Lighting- harsh white lamps from Redpower ect, or a grimier darker look with lanterns from Railcraft or Immersive Engineering.
If you're going ultra modern- use a lot of white, bright lighting, big clean open space with minimal clutter (use tesseracts or hidden piping).