Other than the obvious (my top 6 favorites being Notre Dame, the Duomo's in Milan and Florence, St. Peter's in Rome, St.Mark's in Venice an Sagrada Familia in Barcelona) what do Fodorites consider the top churches they have seen or think are worth visiting ??

Westminster Abbey, Chartres, the cathedral at Rouen. And, of course, Ste. Chapelle.

Assisi - Basilica of San Francesco
Padova - Basilica of St. Anthony in Padova
Pompeii - Basilica of our Lady of Pompeii
Lourdes
Malta - St. John's Cathedral or Mdina Cathedral
St Stephen's Cathedral Vienna
Seville Cathedral Portugal
Cologne Cathedral Germany

Lincoln Cathedral
York Minster
Bodø cathedral and Hammerfest Church - both modern, stark and beautiful.
St Mary Tal y Llyn and St Cwfan's Church in the Sea, both in Anglesey.
Grote Kerk, Naarden.

In addition to those mentioned already:

Venice - Santa Maria Gloriosa dei Frari
Rome - San Giovanni Laterano
Santa Maria del Popolo (for Caravaggio paintings)
Santa Maria Sopra Minerva
Siena - Duomo
Florence - Santa Croce
Prague - St. Vitus Cathedral

For the exterior/setting/location:
Paris - Sacre Coeur
Mont St. Michel - Church of Mont St. Michel
Prague - Church of Our Lady Before Tyn
Venice - Santa Maria della Salute
Pisa - Duomo
Rovinj, Croatia - Church of St. Euphemia

Ste Chapelle
Strasbourg cathedral

plus Beagle Bay church in Beagle Bay WA

My favorite in Europe is the Duomo in Siena, with La Sagrada Familia in Barcelona a close second.

I agree with all 6 you have listed, the Milan Duomo being my number one. I would add:

Strasbourg Cathedral
Toledo Cathedral
Cologn Cathedral
St Chapelle
Stephansdom in Vienna

We are going to see the Chartres cathedral and Mt St Michel soon. Can't wait.

Nygvic:

I suggest expanding your topic to "Places of Worship"...for example there are beautiful, historic and interesting synagogues (sinagogas), Buddhist temples, and a variety of Islamic mosques throughout Europe...and world-wide.

The key word is "ecumenism."

I will add:
Il Gesu(Rome).
Hagia Sofia(Istanbul); at present classified as museum; but really a church; unforgettable.
Il Patrarca(Valencia).
Santiago de Compostela Cathedral(Spain).
Saint Peter Church; Salzburg; in a little cemettery, coming down from the castle, baroque at its best, if I remember well.

The Seville cathedral, for sure
Siena and those wonderful floor mosaics
The abbey church in St. Gallen, Switzerland
Hagga Sophia
The Blue Mosque
The Church on the Spilled Blood, St. Petersburg

Tower.....you are right and I appreciate the comment. I chose too narrow a phrasing. Indeed there are many "Places of Worship", such as the Blue Mosque in Istanbul to name one example, that are worthy of visiting and beautiful.

Seville was in Spain not Portugal, last time I looked !

It all depends on what you're looking for.

A couple of the most fascinating I have found are:

San Celemente in Rome - you can descend through multiple different layer of the church to the Templ of Mithras at the bottom

Church of Santa Maris Assunto on Torcello (Venice) originally from 6 something (this was one of the islands on which the locals hid to escape the barbarians coming over the Alps to destroy Rome. Very byzantine in style with incredible tile work.

On roads less traveled:

The cathedral in Syracusa Sicily – built around the remains of huge columns which were once a Greek temple

The Carthusian Certosa di Pavia – beautiful monastery near Milan

The Baroque churches of Salzburg, Austria

Birnau Church on Lake Constance, Germany

I'm not as widely travelled as many posters here, but so far my favourites have been:

Sienna - the Duomo
Rome - Santa Prassede
Paris - St Denis
London - St Bartholomew the Great
Strasbourg - the Cathedral

Some of the many that made my jaw drop include (only listing those that have not yet been mentioned):

the stave church in Borgund
Wells cathedral
Vierzehnheiligen
Gustav-Adolf-Kirche in Berlin
Frauenkirche in Dresden
San Vitale in Ravenna

I don't think anyone has mentioned the Wieskirche in southern Germany.

Ely cathedral
Salisbury