Auberge du Poteaupre (Chimay). Nuetnigenough (De la Senne - not really associated, but they have all of their beers and their logo's are alike).
The monthly open brewing day at Brasserie à Vapeur -- not a restaurant but excellent homemade beer cuisine and cheese, really labored over and proudly presented. So few breweries that I've been to here (which isn't an outlandish number) have had anything like real food. I do vaguely recall something approximating a decent cafe menu at Caulier. It's actually about the only time I can remember really eating well at a brewery in Belgium. I do occasionally have the thought, while at a brewpub in the US or elsewhere, 'wow, we (in Belgium) are not great at this.' I like Nuetnigeough but don't think they're really associated enough for this thread. I guess Molenhof qualifies but it hasn't occurred to me to eat there for some reason.