So you have this giant chunk of entities that you plan to reuse in your map (maybe some sort of a per-player system). Hopefully, you've prefixed all of the keyvalues in each ent with something like "system1_". Maybe you have about 100 keyvalues to change, just so you can have a duplicate set of ents prefixed with "system2_". Going through each keyvalue in hammer would take forever, and you know you're going to mess up a few times and break the map.
The solution? Duplicate your .map or .rmf and open it up with Notepad++ (WARNING: Saving an .rmf with a text editor other than NP++ might break the .rmf. Editing .maps is the safest). Press Ctrl+f and replace every instance of "system1_" with "system2_". Save it, and open the duplicated map in hammer. Copy and paste the renamed ents into your unaltered map. BAM! hours of work compressed into seconds.
A couple of experienced mappers I know were unaware you could do this, so I figure posting this will help others, too.