Choosing the right school

Very little. You should find that the free schools have a specific religion lesson in line with the school governance and that the Go! schools have a choice of religion(s) or not.

To a Belgian with a partisan view of the political and social history of the country, it's more a matter of who you don't want to have control over your children - church or state, and therefore tends to be a clear decision steeped in family history.

Yes, what J said, but these days there isn't that much difference even in that sense. Most 'Catholic' schools will (also) deal with non-Christian subjects during their religious classes.

Catholic schools have a slightly better reputation since, technically not being state-run (only heavily subsidized), they can be somewhat more exclusive - but that's a generalization. You should always research the individual school before sending your child there.