Heading to Amsterdam from the 16th- 23rd. Trying to decide a few other stops during that time-frame. Never been to Amsterdam or Bruges so definitely want to see those. My wife and I did a brief stint in London and Paris during our honeymoon but want to head back for a little more exploring. Still deciding between the two. Here's our current thought:

16-18 Amsterdam
18-20 Bruges
20-22 London (or Paris)
22-23 Amsterdam (we fly back home from amsterdam, so thats why we are returning)

so basically 2 nights everywhere
but our last night in Amsterdam

Ive taken eurostar for the london to paris trip on our honeymoon, not sure what Ill do for the other ones, as I know eurostar doesnt do bruges or amsterdam ( i dont think)

Eurostar will happily sell you tickets from Bruges or Amsterdam to London. However, in both cases, you'll be taking someone else's train as far as Brussels, then a Eurostar onwards. You're looking at a ~4 hour journey from both

(Eurostar were set to launch a service to Amsterdam, but then the Germans were very late delivering the new trains, which won't enter service until December at the earliest. Eurostar are still talking about doing it, but without a lot of details yet, especially not about how they'd handle immigration and security checks at busy stations, and how they'd handle Schengen-"domestic" passengers)

Given the airport options available (or not) near Bruges, I'd probably still look at Belgian domestic train + onwards Eurostar from Brussels, on a through ticket booked with Eurostar. I'd probably fly back to Amsterdam in your situation.

Another option, only slightly slower - morning train from Bruges to Lille, nice lunch in Lille with a short wander round (there's left luggage at Lille Europe station), then shorter Eurostar trip from Lille to London.

You can take a local train from Bruges to Brussels or Antwerp (I forget which is closer), and then the Thalys high speed train to Paris 1.5 -2 hours. Then to get back,ttake the Thalys again directly back to Amsterdam (about 3 hours). If even stops straight at the airport if you prefer to spend the last night in Paris instead of Amsterdam. Just leave plenty of time in case there is a delay.

From Bruges to London you could consider the Eurolines bus. Quite cheap, not fast (takes at least 6 hours). Channel ferry is an experience.