Fines at commune?

That is not good at all...
There may be some legal twist to avoid having to pay too much but it may be difficult to demonstrate that he did not know. Good faith may not be sufficient here.
For starters, they may ask him to pay for all the commune taxes he did not pay until now. Then if he has been working in Belgium but did not pay taxes because the Belgian State did not know he was there, they will ask for something as well. etc.
Fines may come on top of it for dessert :-)
Once he registers to the commune, the State will know that he's in the country and will analyse his situation very carefully.
I did not register to the commune when I arrived because there is nothing similar in my home country, and I really had no idea that I had to do so. I solved it all after changing home, as I had a new renting contract to show to the commune and I happened to change job at the same time. They never asked for more :-)
Anyway, he needs to analyse carefully his situation to see if there is any trick to use... otherwise...

Just wondering how someone could live here for so long without the most basic knowledge of knowing they must register with the commune? Never been to doctors? Never opened a bank account? Never bought a season ticket for STIB? Please tell me this is a wind-up.

When I got over here first I did not register for almost 2 years.
Nobody told me I needed to do this.When I got here I already had a BIZ number organized by my employer so I thought that was all I needed. I had managed to open a bank account, get mutuality and rent a property using my passport and work contract.
I was also paying tax from the first day I worked so I didn't think anything was wrong!
When I got together with my girlfriend however,she explained that I needed to register with the Stadhuis.
As soon as she told me about it I went to the local VVV and explained my situation, they were very helpful and after a little delay with the werkagent ( the cop that comes to make sure you are living where you claim you are) I was issued with my ID card and I had only to pay a small amount ( I think it was the yearly commune fee that I had not paid since I wasn't registered the previous year)

If he explains his situation he should be ok, but if he was working in black money then he may have issues as he would have no legal wage and possibly no legal address.

It might be better if he says he's been here five months rather than five years!

I find it pretty hard to believe that anyone could have lived here for five years and been completely unaware of the need of registering?