In Tintin and the Mystery of The Golden Fleece
, the part of Marlinspike is played by the Château de Villette
at Condécourt, possibly better known now for being featured (as itself) in The Da Vinci Code
Although the scenes on the surface of the water with the boat took place in Greece and Turkey, the underwater footage was filmed at Lavandou, on the Côte d'Azure.
As well as Athens, the Greek locations were around Loutraki, which is on the Gulf of Corinth, and Ireo, an old port on an island close to Turkey.
The monastery where they visit Father Alexander appears to be Monastery of the Holy Trinity, one of the six "Meteora Monasteries" ("Monsatries in the Clouds") near Thessaloniki; I say appears
to be, as there are certainly shots of it in the film, looking up, but never having been there, I don't know if it was all one location, or if they used multiple locations, because they all look quite similar.
There are of course many locations around Istanbul, including the Blue Mosque, the Golden Horn and its docks, and the Rumeli Hissar, the castle where Tintin climbs down the tower on a rope. The spelling of this last place seems to vary quite a lot, so you might find it under slightly different versions (but it is also called Boğazkesen Castle in some places, so it's a place of many names!).
Interiors were filmed at studios in Boulogne-Billancourt, Paris.
Hope this helps to get you started!Update:
Oh, and one little thing which puzzled me for a long time... In the background to shots of The Golden Fleece
at its moorings, you can see a tower on the far shore which should
be easily identifiable: it's got a row of arched windows near the top, and a little sort of turret thing on the roof. However, scanning photos and maps online, it was not possible to match - until...
It's the Galata Tower, a cylindrical tower with a distinctive high conical roof, built by the Genoese in 1348, and a prominent landmark near the junction where the Golden Horn meets the Bosphorous.
So why the problem?
Well, what I didn't know was that the "distinctive" roof was actually destroyed in 1875; it didn't get it back until renovation work in 1965-67, which post-dates the movie being made. So the tower as seen in the film is not how it appears today.
As a result, I'd hazard a guess that The Golden Fleece
is moored somewhere along the waterfront where the modern ferry terminal sits, looking across the inlet at the tower, but I'm not certain, as modernization has changed much of the look of the place.
Another little note of interest, although not entirely related, is that in the scene where Haddock is menaced by the rolling wine-barrel, before it hits the market stall, the sequence is at least three distinct takes. If you look behind Georges Wilson in the wide shot as the barrel is bearing down on him, a net has been strung across the street slightly further down (it's much clearer in the book, but is visible on video), presumably to catch the barrel - this was no doubt safer, more controlled, and also easier for the crew if there was a need for retakes. It isn't there when in the establishing shot which shows Haddock walking in front of Tintin down the hill, but has been put in place when Tintin tells the Captain to watch out, then disappears in close ups of Wilson reacting. Presumably the barrel was caught, the unit then moved down the street and set up for shooting the stall, at which point the barrel could be released for the next stage much further down the hill.