I used Word and Endnote to handle the citations in my PhD thesis. It did the job well, but I had to disable cite-while-you-write because after a few hundred (or thousand) references, it became too slow and sluggish, even on a Core i7 with 8 GB RAM. I chose to play safe using this software, and I wonder whether I would have a better experience by using other software. Zotero seemed to be particularly good, but when I found that out I had done almost all my references with Endnote already...