I use BibTeX when I write papers, and sometimes it is necessary to merge two .bib files into a single file. One cannot simply paste file A into file B if the files contain duplicates. The best solution I’ve found so far is a program called BibDesk for Apple OS X. It allows you to drag and drop the contents of entire .bib files. I’ve used it to combine all my files into one big file (which still contains duplicates), but then I can select Database : Select Duplicates or Database : Select Duplicates by Cite Key. At this point I manually delete the duplicates, which is slightly annoying since I have to unselect one of the duplicates lest I delete both copies of a particular entry. Hopefully I just haven’t discovered a better solution yet.