I think a friend of mine once told me there were some LoTR/Silmarillion parallels in B5, sort of like the wars of the First Age in Silmarillion projected onto a cosmic backdrop. Had you noticed anything like that?
I can see that, but probably the only conscious nod to Tolkien was the name of a group that first appeared in Season 2 and played a major role in the series from then on: the Rangers. The backstory of the series really owes much more to the "Lensman" series written by E.E. "Doc" Smith in the 30s and 40s.