1. Used of hardware or software designs, implies "elegance in the small", that is, a design or implementation that may not hold any surprises but does things in a way that is reasonably intuitive and relatively easy to comprehend from the outside. The antonym is "grungy" or crufty.
2. To remove unneeded or undesired files in a effort to reduce clutter: "I'm cleaning up my account." "I cleaned up the garbage and now have 100 Meg free on that partition."