Thanks everyone for the great suggestions! Maastricht and the flower auction are definitely on my list now! We might take a weekend trip to Brussels and Bruge.
Liirogue, I hear Polar Bear can take you on quite a trip.
Yeah, I don’t think so… I’m totally doing a Red Light District tour, but not in the way Polar Bear would go about it!
Aw come on! Would you visit Manhattan’s Little Italy and not eat out at an authentic New York Italian restaurant?
Not anymore, A ban on the smoking of tobacco - but not marijuana - in cafes, bars and restaurants has comes into force in the Netherlands.
Very small cafes are allowed to have smokers, but those should be the exception
The Stederlijk modern art museum is also in Amsterdam and well worth a visit. I actually enjoyed more than the Rijksmuseum (seen one Night Watch…).
I’ll second Leiden, home to the Netherlands oldest university with many good museums. I was blown away when I went to the Archaeology museum – for a start the first thing you see is a actual (if bijou) Egyptian temple rescued from the Aswan Dam.
The railways in the Netherlands are excellent. And on cold winter days be sure to sample the poffertjes, little pancakes sold by street vendors. I will warn you though, after a few weeks you will pine for the hills and get excited by tiny mounds and sea dunes.
Thirding Maastricht.
I personally also like really like Den Bosch ('s Hertogenbosch, to give it its proper name). It’s probably too small to warrant a large detour, but as it is quite central you could do much worse than go there for a ramble, some pleasant shopping and a Bosche bol (a kind of giant profiterole).
If art is your thing the Kroeller - Moeller is fabulous. It is also in a nice nature park.
I agree with Bruges. Cologne in Germany is also an option. Admittedly the town centre isn’t very interesting but it has a spectacular huge gothic cathedral, great beer and IMO some of the nicest folk in Germany. What more could you ask for?
I was there a few years ago. There are organised toursthat you can book from your hotel.
I liked The Windmills tour, and Holland in a day
There is an organised tour of the red light district available.
For dining I hear good things about The Green Lantern/ De Groene Lanteerne
It does an excellent fondue, I hear, and is reputed to be the narrowest restaurant in the world. (It was closed for refurbishment on my trip, sadly, so I didn’t get to eat there)
tnx
Which is in Amsterdam. Which needs specifying as Švejk already said upthread. Yes, we are a small country, but The Netherlands doesn’t equal Amsterdam. We have other nice cities that we have been mentioning. 
True, but the OP has mentioned seeing some museums that are specifically in Amsterdam. Amsterdam is one place that she intends to visit. I therefore think it valid to suggest a restaurant there.
Of course she will and should visit Amsterdam and *of course *it makes sense to recommend restaurants there. What slightly annoyed me was just that you recommended the restaurant without saying where it was (without clicking on the link, that is), as if Amsterdam is the only place in The Netherlands which has restaurants or that one could possibly visit.
Sorry, not meaning to rant. I’m from a “far”* province of The Netherlands and we often feel a bit forgotten -and wrongly so. I hope the OP has a lovely time exploring both Amsterdam and other places.
*By Dutch standards. It would take me 2.5 hours to reach Amsterdam from my hometown. In Dutch terms I’m practically from outer space. 
Seconding (thirding? I lost count) the Archeology museum in Leiden; And the Stedelijk Museum for Modern Art in Amsterdam. The Stedelijk is currently closed for reconstruction, but the collection is on exhibit in different locations all over Amsterdam.
Also recommended in november; the railway museum in Utrecht;
The Tropenmuseum in Amsterdam. A museum about Hollands rich colonial past and about exotic cultures.
Also nice in Amsterdam; a combined visit to the science museum Nemo, shaped like a ship, combined with a trip to the National Naval museum, across the Amsterdam harbour and acessible by foot bridge.
It is a quiet, small and rather out of the way museum without modern bells and whistles, in an elegant old historical building. It has a small collection. However, the few paintings is does have are masterpieces of superb quality. But most of them will only be appreciated by true art connoisseurs.
Some highlights in Maastricht:
Go to the tourist office and make the city tour. If the weather is awful, take the guided tour in the little trains leaving from the Vrijthof. Also visit Selexcyz, the bookstore in a church.
Visit the Roman remains in the cellar of Hotel Derlon. Go for lunch in the medieval celler with open fireplace in “t Knijpke” ; Indonesian dinner in the Branding.
I went there several years ago as part of a Rick Steves tour. I have little interest in flowers, but the sheer size of the building and the scale of the operation is just amazing. And it was interesting to see a real “Dutch auction.”
We stayed in Haarlem, which is a nice town not far from Amsterdam. And it is where the house of Corrie ten Boom and her family was located.
If you’re not totally into his style, you can probably skip Rembrandt’s house, the Museum het Rembrandthuis. I found the experience not worth the pretty hefty admission. Unless you have one of those package cards (the “museum card”, for example), then it’s much less.
Apart from the paintings, it’s basically an old Amsterdam townhouse full of tourists.
It’s still closed? I was there in 2005, and they had one small wing open, which contained the best works of the museum. I actually enjoyed it more than having to shlep through a huge museum to see the masterpieces.
Madurodam is a huge outdoor minature of the more famous sites and buildings in the country. It’s in Den Haag. There is a beautiful casino on the beach in Scheveningen, which is, I believe, a neighborhood in Den Haag.
There’s also the Peace Palace and the street of embassies.
Hint: take really warm clothes. I was there in August and nearly froze to death.
IMO, the Mauritshuis is definitely worth it–if for no other reason than seeing Vermeer’s A View of Delft in person. His Girl With A Pearl Earring is spectacular too, and of course there are other great pieces there, but I have never been as bowled over by a painting as I was when I stood in front of A View of Delft.
I’ve never seen an actual painting that’s been so much more powerful than any reproduction of it. I think the manner in which it is displayed–mostly the lighting and the room it’s in–may have a little to do with it… I don’t know… but the damn thing seems to glow from within.
It’s pretty easy to get around the part of the NL that you’ll be in. Utrecht and s’Hertogenbosch are 20 - 30 miles away, and Rotterdam, The Hague, and Amsterdam are not too much further. I enjoy s’Hertogenbosch a lot, but I don’t think most people outside of NL have heard of it.
It’s a shame there is no train station in Waardenburg, but I think you can just take a 10 minute bus ride to get to the nearest train station.