As for those of you, who actually played this game through, would be obvious,
Virlgil leaves the party after our visit to the Dark Elf village. He says, he goes to Caladon.
I run to caladon, search the whole place (yes, even thebasement of sobbing onion), and still cannot find him. Besides his fughting and healing skills, I sorely miss the insanely valuable stuff he was equipped with... :(

If I remember correct you have to talk to someone before you can find Virgil in the Sobbing Onion. I do not remember off the top of my head who though. Possibly check the temple? Maybe Elder Joachim is there?

Did you needle him about his personal stuff beforehand? As in, visit Caladon cemetery, look up the name on the tomb, ask him about it, check the name in the Tarant archives, wait for him to fess up? I'm not sure if it helps, but I certainly didn't have to talk to anyone before going to fetch him in that basement.

Alternatively, load up an old save and strip him naked before that moment.

I recall visiting the cemetary, which made him all emo, and of course, as a good friend I am I asked him about it. I'm not sure I checked said name in the Tarant archives though. I'll do that, hoping it will help. If that doesn't help, I'll look forward for the touching scene of him running away dramatically in his underpants.

If it's any help or comfort, this makes him a better (and less annoying) person.

Oh, I still have Magnus. His constant bitching made Virgil totally unnoticable.

Just go back to the Dark Elf village and make sure he actually, definitely left. It is not unknown for him to become trapped by the trees.

This is hilarious.

He just loves those trees so very, very much...
Remind me to strip him down to skivvies before he does that next time, so that he goes running naked into the woods to embrace nature.

Not sure if you had success with this yet, but I think before you can find Virgil you need to have done 2 things. (1) Visited the Caladon graveyard and spoken to him about his sudden exit. (2) Go to Tarant and enquire at the Archives about the person mentioend on the Gravestone that Virgil visited while in Caladon. You will be given a newspaper, and I think you probably need to read it before you can find Virgil in his appointed spot.

You have to discover the truth about the Panari church and then Virgil will appear in the basement