Do you mean the Argentinian/Brazilian or the Paraguayan WHS?

My selection:

Abu Mena
Meteora
Monasteries of Daphni, Hosios Loukas and Nea Moni of Chios
Mount Athos
Reichenau
Santa Maria delle Grazie
Saint Catherine Area

The situation so far

Meteora (iconic)
Mont Saint Michel (iconic)
Mount Athos (iconic)
Rila monastery (best example in the region and iconic)
Saint Catherine (iconic)

with 2 or more votes
Santa Maria delle Grazie (Leonardo da Vinci)
Scelig Michel
Abu Mena
Flemish
White Monuments of Vladimir and Suzdal

with 1 vote but good reason

Abbey of St. Gall -- home to a renowned library, which is one of the world's oldest and richest

Churches and Convents of Goa - Y - introduction of Catholicism to India; representative of Portuguese colonization efforts

Belem- Iberian
 

Others with 0 or 1 votes
Stari Ras and Sopocani
Abbey and Altenmünster of Lorsch
Armenian Monastic Ensembles
Benedictine Convent of St. John
Cistercian Abbey of Fontenay
Convent of Christ in Tomar
Corvey
Ferapontov Monastery
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
Medieval Monuments in Kosovo
Monasteries of Daphni, Hosios Loukas and Nea Moni of Chios
Monastery of Alcobaça
Monastery of Batalha
Monastery of Geghard
Monastery of Horezu
Novodevichy Convent
Pannonhalma
Poblet Monastery
Popocatepetl monasteries
Qadisha Valley
Reichenau
Residence of Bukovinian and Dalmatian Metropolitans
Saint-Savin sur Gartempe
San Antonio Missions
Santa Maria de Guadelupe
Solovetsky Islands
Studenica Monastery
Trinity Sergius Lavra
Yuso and Suso Monasteries

I'd like to re-emphasize Belem (which I believe received more than just one vote since it was mentioned in several threads). If there's one site from Portugal that should make it to the Essential 400, then it's definitely that one. It's the symbol of Lisbon, the symbol of the Portuguese era of Discoveries, the quintessential site for Manueline architecture (the Portuguese variation of Gothic architecture). I would find it weird if the Pico vineyards "continue" but this site does not...
(And ok, I'm biased because I'm Portuguese, but I did refrain from pushing the other Portuguese sites...)

I think that is pretty justifiable on Belem, also our little green man can have some Pasteis de Belem, an integral part of any world tour.

Oh yes meltwaterfalls! Whenever I think of the OUV of Belem at first glance, I think of the fabulous sunsets I enjoyed there eating one pasteis after the other and rinsing my throat with a bottle of Super Bock (apart from the official UNESCO OUV criterion, obviously!)

I would go for:
Belem
Cistercian Abbey of Fontenay (to represent early monasticism)
Flemish Béguinages
Haghpat and Sanahin
Jesuit Missions of the Chiquitos (I think we should choose at least one mission site, this one might be the most authentic but maybe not the most representative)
Meteora
Mont-Saint-Michel
Mount Athos
Rila Monastery
Sceilg Mhichíl
Trinity Sergius Lavra (I also believe we should leave at least one Russian-Orthodox in, and as the spiritual centre of the Russian Orthodox Church this seems to be the one)
Saint Catherine Area

Meteora ("columns of the sky')
Mont Saint Michel ('Wonder of the West')
Sceilg Mhichíl (remarkable environment)

Wrapping this one up. We have been very strict on this category, but probably rightly so because of gross over-representation:

Stari Ras and Sopocani
Abbey and Altenmünster of Lorsch
Abbey of St Gall - home to a renowned library, which is one of the world's oldest and richest
Abu Mena - Coptic church (oriental rites), frescoes
Armenian Monastic Ensembles
Belem - one the most iconic sites in the Iberian peninsula and important also for travel and trade history
Benedictine Convent of St. John - Ottonian frescoes
Churches and Convents of Goa - introduction of Catholicism to India; representative of Portuguese colonization efforts
Cistercian Abbey of Fontenay - to represent early monasticism
Convent of Christ in Tomar
Corvey
Ferapontov Monastery - best representative of mediaeval Russia?
Flemish Béguinages - focus is on female religious worship
Franciscan Missions in the Sierra Gorda
Gelati Monastery
Haghpat and Sanahin
Island of Patmos - representative of Orthodox pilgrimage site
Jesuit Block and Estancias of Córdoba - best example of monumental complex in South America
Jesuit Missions of the Chiquitos - unique vernacular style, representative for missions
Jesuit Missions of the Guaranis - seems like the most relevant group of "missions" in South America
Jesuit Missions of Trinidad and Jesus
Maulbronn Monastery
Medieval Monuments in Kosovo
Meteora - most visually striking group of monasteries on this list
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 - stunning location in a bay
Mount Athos - This holy mountain in Greece is the spiritual center of the Orthodox Church
Novodevichy Convent
Pannonhalma
Poblet Monastery
Popocatepetl monasteries
Qadisha Valley
Reichenau
Residence of Bukovinian and Dalmatian Metropolitans
Rila Monastery - best example in the Balkans outside Greece
Saint Catherine Area - One of the world's oldest monasteries, at the foot of Mount Sinai
Saint-Savin sur Gartempe
San Antonio Missions
Santa Maria de Guadelupe
Santa Maria delle Grazie - home to Leonardo da Vinci's iconic The Last Supper
Sceilg Mhichíl - wonderful setting, exemplifies monastic isolation
Solovetsky Islands - representing Russian monasticism in hostile landscape
Studenica Monastery
Trinity Sergius Lavra - spiritual center of the Russian Orthodox Church
White Monuments of Vladimir and Suzdal - for Russian architecture in general
Yuso and Suso Monasteries

St. Gall should be a maybe. I think it wasn't included by mistake.

I only see it mentioned by Colvin (so 1 "vote"), or is there someone else

Right, my mistake.