The most important thing I've found is making the space larger than you think you may ever need so it gives you room to expand as needed. You WILL end up filling that space, though, so be prepared to make another level to your machine room.
As far as layouts, for one block machines, I do this design:
Specifically, it is a buildcraft pipe (it doesn't matter what kind, but I usually alternate cobble and stone for the look) with a gate that is detecting items in inventory and if so send redstone signal. On it is a facade (iron block in this case), and then a light grey light (non-inverted).
Below that is a project table, and then below that is the machine.
The project table is used to store stuff for in-process work on those machines, and the light reminds you that stuff is in there.