Belgium in 2 days

Gent. Brugge is an open-air museum. Brussel is an acquired taste. Gent is a lively and manageable city and, in case you've seen it all in two days, only 30 mins from Brugge and Brussel on very frequent trains.

"I was between Brussels, Ghent, and Bruge."

I'll just complicate things further, and add Antwerp to the mix.

The question of which of these four cities is the best base, not to mention which is the best, is perennially debated. You won't know how you feel about that until you've seen all four. All I can do is give my personal reactions (below), and advise you to read as much as you can about each one, to see if one seems more appealing to you on your short visit.

Personally, I loved Antwerp, liked Bruges a lot (yes it's very touristy, but you can find quiet corners too), was slow to warm to Ghent but liked it enough by the end of my day there, and found Brussels a snooze except for my wonderful Art Nouveau tour with ARAU: http://www.arau.org/en

Logistically, Ghent is between Bruges and Brussels, and it's only about an hour from Bruges to Brussels, so you can visit all three from a base in any of them. And getting to Antwerp doesn't take much longer. Trains on all these lines run 1-2 times an hour and are unreserved, with no discount for advance purchase. In other words, wherever you end up staying, you can go to any of the others on the spur of the moment, even for just part of a day, easily and cheaply. So don't worry so much about choosing the "right" one.

I'll just add that if you want to see "beautiful sites" and you're staying in Brussels, be sure to limit your sightseeing to the very center. The Grand Place is indeed grand, but most other parts of the city range between "meh" and "feh" in appearance. That's why the Art Nouveau tour was so valuable - the gems are scattered, and the nondescript (and sometimes, downright ugly) is everywhere in Brussels. For eye candy, definitely choose one of the others..

Trains on all these lines run 1-2 times an hour
On weekdays it's more likely to be 4 times an hour.

As a base I vote for Ghent. Not too big not too small not too touristy. But definitely check out Antwerp

You will have the best time in Antwerp, second choice Gent. In the unlikely event you get bored, the train to any of the other big four is cheap and fast, for a daytrip - no need to change hotels.

You didn't give the total number of days, or the departure airport. If BRU, allow time to get there, it's not the same as going to downtown Brussels. There is an excellent hourly bus from Antwerp to BRU. As you acknowledged, you are going to spend a lot of time on the train, or in bargain airline security lines. Remember that every change of city takes at least half a day. Are you going to Cologne or to Berlin? Big travel time difference. Cologne is well-connected to Belgium and Amsterdam.

Depending on one's interests, you could say that the best places in Belgium are Antwerp, Bruges, Gent, and Brussels. That's too much for 2 days. I think you made clear in your OP that beer and waffles are more important than museums. (Not slamming, just asking.)

We are actually flying out of Paris. So we were going to go back to Paris after Belgium to stay by the airport there for an early morning flight.

So I'm getting the feeling everyone things Antwerp is a definite place to see? We planned on doing Thursday-Saturday for Belgium, coming from Amsterdam for 2 days.

I love the ideas and everyone's opinion!

Antwerpen or Gent.
Don't forget to arrange your Thalys tickets to Paris in time. Advance buying gives considerable discount. The same is for the Thalys service from the Netherlands to Belgium, unless you prefer the Intercity train.

The Thalys departure is from one of THREE downtown Brussels stations. It's not the one closest to the tourist sights, it's Midi/Zuid (French/Dutch, alternating on the columns in the underground station.) When you go online, investigate whether the Thalys "Any Belgian Station" might save you money or time in getting to the train from another city than Brussels. Any train ticket to or from Brussels by any means, INCLUDES all three of those downtown stations - that's NOT what I mean by "Any Belgian Station."

It is unlikely that the Paris station it goes to has the Paris airport train, BTW. I don't remember.

Too bad you couldn't get an Open Jaw air ticket and save this backtracking, for more sightseeing time.

There is also a direct Thalys service to Paris from Antwerpen with a more or less hourly connection. Advance bought ticket can be as cheap as € 29.

The Thalys from Brussels uses Gare du Nord in Paris, which does have a direct connection to the RER train to CDG.