Military/fortification (43):
http://www.worldheritagesite.org/categories/category18.html

Agra
Bahla
Belfries
Bellinzona
Brimstone
Castel del Monte
Crac des Chevaliers
Dacian fortresses
Defence line of Amsterdam
Derbent
Diyarbakir
Durham
Elvas
Shalamar
Fort Jesus
Vauban
Carcassonne
Suomenlinna
Gold Coast (Accra)
Limes
Great Wall of China
Gwynedd Castles
Hill Forts of Rajasthan
Himeji-jo
Hwaseong
Kaiping Diaolou
Kazan
Kernave
Kronborg
La Fortaleza, San Juan
Malbork
Masada
Mazagan
Mir
Namhansanseong
National History Park, Haiti
Portobelo/San Lorenzo
Qal'at al-Bahrain
Quseir Amra (??)
Red Fort
Rohtas
San Pedro de la Roca
Tower of London

Long category... unsure about the Indian and Caribbean sites

Agra - Maybe - not sure whether its main feature is its military function, or rather its palace function; also unsure how to rate it vs Rohtas fort or Red Fort.
Bahla - Y - looks like one of the most impressive Middle Eastern castles / forts
Belfries - N - military function was not primary function of the belfries
Bellinzona - N - prefer other European fortifications
Brimstone - N - prefer other Caribbean / LatAm fortifications
Castel del Monte - Y - iconic medieval castle with mystical undertones
Crac des Chevaliers - Y - major Crusader site in the Middle East
Dacian fortresses - N - of niche interest
Defence line of Amsterdam - N - obscure and niche site
Derbent - N - looks less impressive than other Middle Eastern fortified cities
Diyarbakir - N - the military aspects alone do not seem unique / impressive enough
Durham - Maybe - not sure whether it was already selected in one of the myriad Christian categories; combination of military and religious function is certainly interesting
Elvas - N - prefer Vauban as the quintessential European fortress site, in addition to some other iconic European castles
Shalamar - N - as for Agra, it looks more like a palace site rather than a military site; prefer the Rajahstan forts
Fort Jesus - N - Accra seems broader and more relevant
Vauban - Y - quintessential site for European fortress building
Carcassonne - Maybe - very picturesque site, but "brushed up" by Viollet-le-Duc
Suomenlinna - N - a bit niche
Gold Coast (Accra) - Y - selection of colonial castles and forts, from different European nations, including some of the oldest in Africa
Limes - Y - for Hadrian's Wall
Great Wall of China - Y - iconic and universally known
Gwynedd Castles - Y - probably most impressive series of castles of medieval Europe
Hill Forts of Rajasthan - Y - iconic forts well-known beyond India
Himeji-jo - Y - the quintessential Japanese castle
Hwaseong - N - while I personally enjoyed it, it does not seem to be Top 200 material for me
Kaiping Diaolou - N - exquisitely eccentric, but a bit niche, I'm afraid
Kazan - N - for kremlins, I'd go for Moscow
Kernave - N - obscure and niche
Kronborg - N - more palatial than military; prefer Frederiksborg (which is not a WHS); Hamlet connection not enough
La Fortaleza, San Juan - Maybe - unclear how it ranks vs. e.g. Santiago de Cuba or Caragena (which is not in this category)
Malbork - Y - most impressive brick castle in the world
Masada - Maybe - iconic Israeli site, but mostly associated with the mass suicide of its defenders
Mazagan - N - niche and not very impressive
Mir - N - niche
Namhansanseong - N - seems a bit niche
National History Park, Haiti - Y - I believe I already selected it in another category; rather than for its pure military merits, I would select it as a monument to Haiti, the first post-slavery nation in the Western hemisphere
Portobelo/San Lorenzo - N - other Caribbean / LatAm sites seem more impressive
Qal'at al-Bahrain - N - prefer Bahla for Middle Eastern Forts; also, Portuguese forts would already be covered via Accra
Quseir Amra (??) - N - more a palace than a military site, I believe
Red Fort - Maybe - see Agra. Unsure which to pick for this category between Agra, Red Fort, Rohtas, Lahore (Shalamar)
Rohtas - Maybe - see Agra
San Pedro de la Roca - Maybe - see San Juan
Tower of London - Maybe - less impressive than the Welsh castles, but iconic symbol of London

In general, I second Khuft's recommendations. Unlike him I would plead for a Yes for both Masada (not for its iconic historical role, but for its imposing location in the midst of the desert high above the Dead Sea) and Kaiping Diaolou (a great example of vernacular architecture, largely missing in our list and representing human creativity). I also change Tower of London to a No and second a Yes for the missing Moscow.

My selection

Crac des Chevaliers - major Crusader site in the Middle East
Defence Line of Amsterdam
Vauban -quintessential site for European fortress building
Masada- Built for fortification against Mighty Romans
Dacian fortresses- Ancient Military
Suomenlinna (Also fits here)
Accra
Frontiers of the Roman Empire
Hill forts of Rajasthan
Great Wall of China - iconic and universally known
Himeji-jo


Agra can be better representative of entire medieval South Asian History.
Lahore was capital for mere 13 years where as Rohtas was built during short life span of Sher Shah (and never has much impact in South Asian history). Red fort, Delhi was built by Shah Jahan and we can only see late Mughal Architecture (which are not that much beautiful).
On the other hand Agra was capital throughout Medieval era and example of whole range of architecture.

Agree with Kuft
Great Wall of China - iconic and universally known
Crac des Chevaliers - major Crusader site in the Middle East
Hill Forts of Rajasthan - iconic forts well-known beyond India
Gwynedd Castles - probably most impressive series of castles of medieval Europe
Bahla - Y - looks like one of the most impressive Middle Eastern castles / forts

Additional Sites
Agra Fort - Its fortifications alone are worthy
San Pedro de la Roca - Best preserved Spanish Fortress in the Caribbean
Bam and its Cultural Landscape - Best Fortified city/town in Iran and worlds largest adobe structure

It pains me, because I love Korean fortresses, but I don't think they are Top 200.

Comments on Khuft's selection - agree unless commented on. I would also comment that there are a number of other Military" sites not included in this category -e.g Quebec, Merv, Bam . This type of structure is not at all "under-represented" and needs a fair culling I feel
Agra - YES - have to agree with kkhanekhan that it is best of the 3 Mogul forts and trumps Lahore and Delhi
Bahla - MAYBE - we just need a little discussion about this and Bam. both mud structures (as I guesss is the Merv Erg Kala) Is there is room for all of these. What concerns me about Bahla is its lack of a significant historical role - so it would get in purely on its construction - even though that is not "unique".
Carcassonne - YES - but not really as a "Military structure" - it ticks a lot of other boxes about townscapes etc
Durham - NO - its castle is of little importance. Although the close juxtaposition of Cathedral and Castle is interesting it either gets in on the Cathedral or not at all!
San Pedro - I just don't feel able to decide between this and San Juan (the only one I have visited). But I guess one of them is needed. Can anyone come up with arguments for either?
Masada - YES. Fortress, Palace, amazing location, oodles of "History"
Delhi Red Fort - NO, as per kkhanekhan and pref for Agra as I think we can really only choose 1 of the 3.
Rohtas - NO. As per kkhanekhan. Have visited it and the walls are very impressive but it is a hollow shell and of little historical significance -it could only get in on its "looks"
Tower of London - I somewhat sheepishly put a case for this - despite the Euro-centricity issue (and possible accusations of Nationalism!!). Castles can "offer" significance in terms of military construction (Size, strength, innovation), impressive siting and historical role (as well as doubling as "Palaces"). I know that the UK seems also likely to get the Gwynedd Castles - but these I feel would be included very much as Military constructions. The Tower of London on the other hand, whilst it has a military significance, and is not unimpressive as a "Castle" per se (particularly in its location at the heart of the City), is far more than that. It iconically symbolises "London" across c950 years - and, to some extent, (whatever might be thought about the merits or otherwise of that country's role in World History!!) "England" - Norman Conquest, monarchy, even, with the Ravens, its very "independence" from other European countries which has been a major strand in European history Just look at where it stands in our most visited list (2nd behind Paris).

I forgot to add my support for Carcassonne too. This is currently the only category where it appears.

I think Khuft and Solivagant have my ideas covered here and I'm happy to see the various merits of the Mughal forts are clarified.

I know there is mention of additional sites missing (Luxembourg also comes to mind) but one that really should be listed here is Spissky Hrad, we only have it under categories most associated with Levoca, which was a later extension to the site. I would even be tempted to give it a yes. It is a quintessential military fortification sitting alongside Gwynedd and Crack des Chevaliers. Perhaps we don't need another quintessential but I think it is worthy consideration.

My selection:

Carcassonne
Belfries
Bellinzona
Great Wall
Hill Forts of Rajasthan
Himeji
Red Fort, Delhi

Why?
Sorry, I don't want to single you out, but I would appreciate your reasons for selecting some sites instead of others. Yes, that takes time, but it might help others frame their own views. In particular, I'm surprised why you would select Belfries under "Military".

These sites get my support:
- Great Wall, world wonder represent many styles of fortification from mountains to desert.
- Bahla Fort, mud fortress with oasis and city wall, a perfect example of fortified oasis.
- Himeji, Japanese architecture for castle is artistic and unique.
- Hill Forts, Rajput architecture is outstanding in its own way and perfect example of fortress palace of Asia.
- Gwynedd, represent outstanding castle and fortress of Europe.
- Lime, Roman wall

I've always wondered why there are so many of these on the list. Maybe because fortifications last much longer than constructions for general use?

Anyway, trying to summarize:

Agra - best of the 3 Mogul forts
Bahla - perfect example of fortified oasis
Belfries
Bellinzona
Brimstone
Castel del Monte - iconic medieval castle with mystical undertones
Crac des Chevaliers - major Crusader site in the Middle East
Dacian fortresses
Defence line of Amsterdam
Derbent
Diyarbakir
Durham
Elvas
Shalamar
Fort Jesus
Vauban - quintessential site for European fortress building
Carcassonne
Suomenlinna
Gold Coast (Accra)
Limes / Frontiers of the Roman Empire
Great Wall of China - iconic and universally known
Gwynedd Castles - probably most impressive series of castles of medieval Europe
Hill Forts of Rajasthan - Rajput architecture is outstanding in its own way and perfect example of fortress palace of Asia
Himeji-jo - the quintessential Japanese castle
Hwaseong
Kaiping Diaolou
Kazan
Kernave
Kronborg
La Fortaleza, San Juan
Malbork - most impressive brick castle in the world
Masada - Fortress, Palace, amazing location, oodles of "History"
Mazagan
Mir
Namhansanseong
National History Park, Haiti
Portobelo/San Lorenzo
Qal'at al-Bahrain
Quseir Amra
Red Fort
Rohtas
San Pedro de la Roca - Best preserved Spanish Fortress in the Caribbean
Tower of London