I will be in Amsterdam for 3 days (one of which will be our jet lag day) and am trying to decide which of these is the best deal. I am interested in seeing the rijksmuseum and the Van Gogh. And possibly the stedlijk. It looks like the Amsterdam pass includes some nice transportation options but does not include the rijksmuseum. Thoughts?
I have already seen the Anne Frank house, so that's not a factor.

If you only want to see those museums then you may be better off just buying tickets online for them, and a 2 or 3 day public transport pass.

amsterdam's centrum is compact - you can walk between most major sights - and the National Museum Card can pay off with just the three museums you mention plus you can come and go and visit many museums you probably would not pay to enter - the Anne Frank House is now covered too - gives priority entry at some popular museums.

Rijksmuseum and all major museums fully covered.

Also good for some old churches in Amsterdam -

http://www.amsterdam.info/museums/museumkaart/

buy it at any participating museum - most folks will not ride trams or the metro enough to warrant the 2- or 3-day transit passes and you may want to take the Museum Boat to get around town too (not covered by transit pass I believe).

The good thing about having the museum card is that you can walk into any of the included museums and look around. If you get bored after ten minutes you can leave, without feeling like you've thrown away the entry fee. I usually get bored in most museums after about an hour and the Amsterdam Museumkaart was perfect for me. I went through enough museums in one day that their total entry fees would have been higher than the cost of the card.

A Museumkaart costs €54,95.
The Rijks, van Gogh and stedelijk are €15 each (at least until November when the Rijks goes up in price.
If you buy e-tickets you can skip the queue for the cash desk. Doesn't necessarily mean you skip the queues completely though.

You can still buy a ticket on the tram or bus from the driver if you don't think you will use them enough to get your moneys worth from a 2 or 3 day pass.

It is possible to book an entry time with the museum pass at the van Gogh, or join the voucherlane - which you also join with an e-ticket.

I agree with buying the individual entrances unless you are certain you are going to see enough venues to warrant one of those "deals."

Depending on where in Amsterdam you are staying, walking to the Rijksmuseum or the nearby Van Gogh is going to take some walking.

A Museumkaart costs €54,95.
The Rijks, van Gogh and stedelijk are €15 each (at least until November when the Rijks goes up in price>

but if doing the Anne Frank House that would make the pass perhaps cheaper than 4 solo tickets and you can waltz in to so so many other places you may not if paying - the Rubens House; the Church-in-the-Attic; Jewish Historical Museum - place you may pass by anyway and could just pop in for a quick look - like the Amsterdam branch of St Petersburg's Hermitage museum branch in a neat old canal house.

Thanks, all. Good arguments have been made for both getting a card and for seeing museums a la carte. I may go ahead and get a pass just to avoid lines and have the flexibility to pop in to museums.

Does anyone know how much a 2 or 3 day transport pass costs?

http://en.gvb.nl/pages/home.aspx

the official site of Amsterdam's transports should tell you how much it costs - but I know from looking that over you have to be riding a lot to make it pay off and again central Amsterdam is compact and walking is so so fun here - a surprise around every corner. You may be using trams and the metro less than you think - depending of course on where your hotel is located.

In any case you need not decide on the transport pass until you get there - no need to pre-order even if possible - hit the GVB office just opposite Centraal Station - get a transport map and ask any questions of the English-speaking staffs. The Amsterdam Tourist Office next door (VVV) - get a city map - there also have several walking tours of various parts of the center of town - again Amsterdam is eminently walkable!

Trams are on the honor system so do not forget to buy a ticket when boarding even though no one else does as they have passes probably - month or longer ones - spot checks IME are frequent with steep fines - not sure they sell Strippenkaart - Strip Tickets that give anyone several rides much cheaper than buying single fares on the tram.

Amsterdam has a newish Chip Card system that may have replaced Strip Cards - I do not think it worth your time with such a limited stay to do the Chip Card thingy.