Those are reasonable questions.
Regarding the first
Algernon Files, it's a generic supervillain compendium originally published by Blackwrym Games for the
Mutants and Masterminds system under the M&M Superlink banner. The concept of the book is that these various villain writeups and backgrounds are presented as files maintained by "Algernon," the Artificial Intelligence device which runs the home base of the Sentinels superhero team (writeups for them also included). For more details about that book, I couldn't do better than this previous RPGnet review:
http://www.rpg.net/reviews/archive/10/10329.phtml
I'm afraid I'm not in a position to answer all your questions about
Fires of War, as I haven't seen it yet myself. However, as I mentioned earlier on this thread, FoW is being printed in two versions, one with M&M Second Edition stats, the other in HERO. A new edition of
The Algernon Files updated for M&M 2E will be issued later this year, with a HERO version released at the same time.
Hopefully someone will be along to answer your other questions.