I use FLAG all the time for Fanficton.net stories. I like that you don't have to download it and that it creates a great table of contents for you. I've never used the other two programs that you've mentioned, but if you want something quick and easy, FLAG is it. Plus with Calibre's Kindle Collections, I can bulk-add new fanfic to my Kindle and it saves me a bunch of time. FLAG has been so good to me that I haven't found a reason to use anything else.