Well you could go back to a save where Virgil is still alive, he's not that essential, but he does have his own story line. Alternatively there's several NPC's depending on your alignment and magic/tech affinity. You can find out about them here:
GameFAQs: Arcanum: Of Steamworks and Magick Obscura (PC) FAQ/Walkthrough by SWCarter, which is the best walkthrough I found for Arcanum.