Altering formations.txt will definitely cause problems. Altering strategies.txt shouldn't cause too much of a problem, because you can alter your empire's strategies within the game. Emporertitle.txt, empirenames.txt, and those like them are only accessed when games are created, so having modified ones on your computer will not cause a problem.
I plan on using the Vorlon Empire ship set.
Edit:
Hmm... seems as if PvK responded at the same time I did. Oh well.
[ 17 March 2002: Message edited by: Imperator Fyron ]