I have 7 large official content .package files so far. I had to split the Build/Buy Mode stuff into two merged files, clothes into three, and hair into two because when I tried to import them all into one and save I got an out-of-memory error. I kept sets together, and am maintaining separate merged files for user-created objects, clothes and hair. I haven't attempted to merge any hacks.
That was my main concern - whether I'd eventually try to merge too much stuff into one package. Do you (or anyone) happen to know what the limit is on that?