Right I hope no one objects but I have tried to break down the massive Religious Structure: Christian category (107!) into some slightly more manageable chunks.
I don't necessarily want people to pile in on it as the focus was on natural sites, I just had a bit of time to do it so dove in.

This batch doesn't really make things much easier as it is still huge (49) but it is those where the main focus is on residential structures e.g. Monasteries, Abbeys (happy for people to break it down further if needed.)

Stari Ras and Sopocani
Abbey and Altenmünster of Lorsch
Abbey of St Gall
Abu Mena
Armenian Monastic Ensembles
Belem
Benedictine Convent of St. John
Churches and Convents of Goa
Cistercian Abbey of Fontenay
Convent of Christ in Tomar
Corvey
Ferapontov Monastery
Flemish Béguinages
Franciscan Missions in the Sierra Gorda
Gelati Monastery
Haghpat and Sanahin
Island of Patmos
Jesuit Block and Estancias of Córdoba
Jesuit Missions of the Chiquitos
Jesuit Missions of the Guaranis
Jesuit Missions of Trinidad and Jesus
Maulbronn Monastery
Medieval Monuments in Kosovo
Meteora
Monasteries of Daphni, Hosios Loukas and Nea Moni of Chios
Monastery of Alcobaça
Monastery of Batalha
Monastery of Geghard
Monastery of Horezu
Mont-Saint-Michel
Mount Athos
Novodevichy Convent
Pannonhalma
Poblet Monastery
Popocatepetl monasteries
Qadisha Valley
Reichenau
Residence of Bukovinian and Dalmatian Metropolitans
Rila Monastery
Saint-Savin sur Gartempe
San Antonio Missions
Santa Maria de Guadelupe
Santa Maria delle Grazie
Sceilg Mhichíl
Solovetsky Islands
Studenica Monastery
Trinity Sergius Lavra
White Monuments of Vladimir and Suzdal
Yuso and Suso Monasteries

Edit: just saw this one was missed off
Saint Catherine Area

Thanks for splitting them. Only few seem to stand out on first sight (Meteora, Mt St Michel, Scelig Mhichil)

Some I would include (other ones I do not know well enough to decide):

Abu Mena - Coptic church (oriental rites), frescoes
Benedictine Convent of St. John (Ottonian frescoes)
Ferapontov Monastery (best representative of mediaeval Russia?)
Jesuit Block and Estancias of Córdoba (best example of monumental complex in South America)
Jesuit Missions of the Chiquitos (unique vernacular style)
Maulbronn Monastery (best example of a cistercian?)
Meteora (iconic)
Mount Athos (iconic)
Mont-Saint-Michel (iconic)
Qadisha Valley (iconic)
Residence of Bukovinian and Dalmatian Metropolitans (outstanding example of art nouveau)
Rila Monastery (best example in the Balkans outside Greece??)
Saint Catherine (iconic)
Saint-Savin sur Gartempe (Romanesque frescoes)
Santa Maria delle Grazie (Leonardo da Vinci)
Sceilg Mhichíl (iconic)
White Monuments of Vladimir and Suzdal (Russian Baroque)

I would also add one of the Portuguese and one of the Mexican sites.

Just saw I missed off one:
Saint Catherine Area

My selection:
Belem (one the most iconic sites in the Iberian peninsula and important also for travel and trade history - Manueline style too)
Gelati Monastery (one of the most interesting Armenian sites)
Meteora (not only iconic but completely unique in the region if not worldwide)
Mont Saint Michel (iconic)
Rila monastery (best example in the region and iconic)
Scelig Michel (outstanding, iconic and in a wonderful setting)
Saint Catherine Area (one of the most important Christian sites in Arabia)

Medieval Monuments in Kosovo
Meteora
Mont-Saint-Michel
Santa Maria de Guadelupe
Popocatepetl monasteries
Rila Monastery
Saint Catherine Area
Mt. Athos

I will put in a case for Mt Athos - as a large independent monastic community encompassing a range of monastic traditions and practices as well as for its architectural and artistic treasures extending across 1800 years. It also covers a range of other generic criteria eg holy mountains.

Why would Rila (for instance) be rated above it?


Regarding the Mexican contenders. When i visited both I preferred the Sierra Gorda examples - later and more indigenous but I conclude that the much earlier Popocatapetl ones which cover the massive and sudden imposition of a new culture are probably more significant.
A south american example can cover the indigenous art/architecture aspects?

Flemish Beguinages? they may be the only site on the list where the focus is on female religious worship, where as the exclusion of women is a strong feature of others.

Conversely when I drew up this list I assumed Mt Athos would be a shoo-in, I'm surprised to see it take so long to be mentioned. I truly love Scelig Mhichil and will happily nominate it, but it is a small outlier, literally and figuratively, in comparison to Mt Athos.

Yes - I would go along with that

Actually I compared Meteora with Mt. Athos and I felt that Meteora should represent Greece. I choose Rila Monastery to represent Eastern Orthodox monastery.

Fair enough, I think that is where listing the reasons for inclusion exclusion would be of use in divining peoples thinking.

Also why did you go for Meteora over Mt Athos? Within the orthodox church Mt Athos is regarded as the most important with Meteora being the second most relevant within Greece?

I am okay with Mt. Athos also ( It also deserves at least nomination in top 200 nomination, I am adding it as another suggestion). Both sites were too good. I just wanted to diversify the list, though I did not include any Asian chruches.

Once again, here is the link to the Religious Structure, Christian category, for anyone who needs it.

This is an extensive list, and only a few immediately stood out to me, either because I've been there or because they are outstanding in architecture, location, or history:

1. Meteora -- Possibly the most visually striking group of monasteries on this list, with a unique defensive location on pillars of rock; I'd love to visit some day
2. Mont-Saint-Michel -- The only visual rival I can think of to Meteora, with its stunning location in a bay on the north of France
3. Sceilg Mhichíl -- This complex off the southwest coast of Ireland exemplifies monastic isolation (well, at least until the Vikings found them)
4. Mount Athos -- This holy mountain in Greece is the spiritual center of the Orthodox Church (but it's only accessible for men)
5. Trinity Sergius Lavra -- This monastery complex northeast of Moscow is the spiritual center of the Russian Orthodox Church
6. Saint Catherine Area -- One of the world's oldest monasteries, at the foot of Mount Sinai

As I read through the reasons for inscription for other sites on the list, I can see why some would be important, and I'd probably add them to the list, too:

1. Abbey of St. Gall -- home to a renowned library, which is one of the world's oldest and richest
2. Maulbronn Monastery -- distinctive example of a medieval monastic complex, and it influenced architecture in northern and central Europe
3. Flemish Béguinages -- highlights the role of women in the middle ages who served God without retiring completely from the world
4. Santa Maria della Grazie -- solely because it is home to Leonardo da Vinci's iconic The Last Supper

There are also monasteries that stood out for their regions, such as Medieval Monasteries in Kosovo (Serbian Orthodox); Monastery of Geghard(Armenian Apostolic); Popocatepetl Monasteries (Catholic, Mexico); Jesuit Missions of the Guaranis (Catholic, Argentina and Brazil); Churches and Convents of Goa (Catholic, India). I just don't know if I would choose any of them if they made it to the list of 400 or so that we are culling down to 200.

This issue of the relative importance of "Visual impact" v "other values" in determining a site's worth is coming up quite frequently under other categories too. Giants Causeway and Jeju for instance - "Columnar jointing" and "Lava tubes" are certainly somewhat "niche" issues within the overall subject of "Volcanism" but those 2 sites really are very impressive to see!!
Similarly with The Meteora
We have tended to use the word "Iconic" in a number of discussions as a justification for selection (indeed sometimes almost as if it is an almost incontrovertible factor!) - this is really a proxy for "Visually very significant" since sites become widely recognised (and hence "iconic") largely because of their visual impact (sometimes of course enhanced by their fame in movies or whatever which itself reflects some aspect of visual impact even if not necessarily "beauty" - I think of Battleship Island here!).
That is not to say of course that "Iconic" or "Visually significant" sites can't possess significant other attributes which fully justify their selection but it does rather give them an "advantage" which may put the less visually significant or well known site at an unjustified disadvantage! (and again I am not saying that this is the case with The Meteora v other monasteries). Take Tassili for instance v Wadi Rum! How many people could recognise a single photo from Tassili?
How much value do other contributors to this exercise feel should be given to "Visual impact" in selecting sites? We may have to explain to the Little Green Man that we humans place great value on often superficial "visual impact"/recognition and that this tendency can overwhelm more objective criteria. Also that this aspect of our psychology impacts our mating habits and even our selection of Leaders!!

There are a few that I would add to those that were mentioned:

Churches and Convents of Goa - Y - introduction of Catholicism to India; representative of Portuguese colonization efforts
Island of Patmos - Y - representative of Orthodox pilgrimage site
Jesuit Missions of the Guaranis - Y - seems like the most relevant group of "missions" in South America
Solovetsky Islands - Y - representing Russian monasticism in hostile landscape
White Monuments of Vladimir and Suzdal - Y - for Russian architecture in general