There are 19
communes (municipalities) in Brussels, and each have a
very different administration. Brussels City has one of the worst administrative centre. Aside from being hosted in an eyesore from the 1960's, there are always long queues at the counters, and most of the people waiting are African immigrants, which gives it a feeling of refugee camp. The civil servants are usually grumpy and seem to enjoy making your life more difficult if they can.
This contrasts sharply with the town hall of Uccle, one of Brussels' richest municipalities, that looks like a little French château, and where you are greeted by a staff in suit and tie and directed to a touch-screen computer to select the service you need. There are almost no queues and service is impeccable (almost hotel-like). They don't fuss over little details or make you fill unnecessary red tape if it can be avoided.
It's also important to know that Belgian municipalities have a tremendous amount of power compared to many other countries. They are the ones who decide whether a foreigner can obtain, modify or renew a visa or work permit. This is usually the privilege of a centralised Immigration Bureau, but not in Belgium. If you know someone in any city, town or village administration, you can easily obtain any visa you want. That's almost scary.
But that is basically why there are so many immigrants queuing in Brussels City, where
one third of the population is foreign, most of which are economic migrants or refugees. Your best bet to avoid the queues is to come a bit before it opens, as most of them don't work and won't bother to come very early.
EDIT : Depending on what you need to do, you could try going to the
Liaison office on Louise Avenue, which is less crowded and better frequented.