Mate References are great for all of those "standard parts" that need to go in what seems every assembly (i.e. nuts, bolts, washers, pems, gears, inserts, and anything else you may use in a lot of assemblies). Mate reference make dragging and dropping parts from the Feature Palette or Windows Explorer and mating them in the assembly possible.
To define a mate reference:
Q: Now that I have set up my "standard parts" with MateReferences, what do I do with them now?
In Tools Options under the System Options there is a sections named File Locations. In here you can set up any directory you would like to look to for these "standard parts". The directory can be a network directory that everyone can share also can be read-only so the files do not accidentally get erased or files get changed.
I have created an animated GIF file here best at 1024 X 768 (a little slow but good) to demonstrate what can be done with the mate references. The example shown is of course with MateReferences but the technique shown can be done with any part file whether it is with or without MateReferences. The same way shown drug and dropped out of the Feature Palette you can drag and drop it from windows explorer or My Computer windows. When the files are drug and dropped from Windows Explorer or My Computer Windows, SolidWorks site recognizes the mate references and mates appropriately.