Let me see...
My first Landsknecht, was named Zeta for a few reasons. Two of them being:
1) looking at the manual back when I got the game, I noticed that "Zeta" was the name of one of the characters. After seeing that, I decided to go with that instead of my previous choice, "Edo".
2) Check my username.
I named my medic Asuna because she reminded me of loli-Asuna from Negima XD
I named my Protector Hazumu because I thought it was a pretty neat androgynous name after reading Kashimashi.
... and as for game characters:
My second Landsknecht, Vacuna, has been with me as a swordsman/pikeman for a number of years now, ever since her name came up during character creation in Disgaea as I was randomizing it with [select].
After a little googling, it turned out that her name was a little more than just a few random characters thrown together:
http://en.wikipedia.org/wiki/Vacuna
My Alchemist Django was named after a character from Boktai of the same name, as he bore a slight resemblance.