In the beginning of watch manufacturing or watchmaking, individual master watchmakers hand crafted one of a kind works of art for royalty.  These artisans like Abraham Louis Breguet would toil for many months to make one timepiece entirely by hand.  These mechanical masterpieces kept accurate time and were hand made by genius artisans.  How incredible it must have been.

In this era of modern technology and mass production, most of the luxury brands that are well known use mass production techniques and their products do not come close to using the hand craftsmanship that the early artisan masters used in the production of their watches.

Companies like Rolex, Omega, Breitling, TAG Heuer, etc., produce extremely large quantities of watches each year and there, frankly, aren't enough artisan watchmakers in the world to produce the large quantities of watches by hand and in the time frame necessary.  Experts have estimated that Rolex produces more than 4,000 watches per day.

Fortunately for collectors and true connoisseurs there are companies who do the hand craftsmanship.  Many of these companies are not in Switzerland believe it or not.  Three of the companies that perform large amounts of hand craftsmanship on their watches are based in the US -- which led the watch industry until lower wage rates in Switzerland and the quartz revolution allowed the Swiss to take over the luxury markets and the once prestigious American brands became extinct or were sold to European or far east owners.

Other small hand craftsmanship style brands exist throughout Europe.  But the group of artisan watch manufacturers is extremely small.  RGM, Montres Allison, and Montana Watch Company in the US perform functions like rose engine turning of their dials and hand finishing their components.  Montres Allison shows pictures and videos on their website of the engine turning process and casting molten 18k gold and platinum watch cases and components for their movements.  RGM has some engine turning pictures and videos and also makes custom watches.

The AHCI at ahci.ch is a great place to learn about some artisan craftsman watchmakers.  They have a good list of mostly European companies, but also include Kiu Tai Yu of Hong Kong. 

Then there is Jochen Benzinger.  Benzinger takes existing movements and completely skeletonizes them and adds precious metal components, hand engraving, and rose engine turning to the components.

Thomas Prescher and Grubel & Forsey have created very complicated variations on the tourbillon mechanism.  You will be lucky to ever find one of their works of art.

These companies and individuals listed above come the closest to emulating the early Breguet style watches built one of a kind for royalty.  Investigate these brands.  One sign of hand craftsmanship is imperfections believe it or not.  If  a watch case is built by hand, it will have some small flaws.  It won't be perfect like one that has been mass produced by the hundreds of thousands.

Hand crafted works of art like these can be a little temperamental -- just like the comments you've heard about Ferrari and Lamborghini and Lotus and Bentley and Rolls Royce.  Especially with watches, the precision has to be incredible.  These artisans do an incredible job of performing microtechnics using hand methods at their finest.

The most valuable watches are not perfect.  They takes months and years to complete, but are beautiful and well made and heirlooms and have not been mass produced via cnc machine in large factories.

Many of these watch companies don't have large advertising budgets so you probably have not heard of them and provide remarkable after sale service.

Please take a look at these guides for the information about the accurate meaning of the term Swiss Made and then look at the mass production of the high end Swiss brands, and you will see that if you want the creme de la creme, you should look for an artisan with a small atelier for your next high dollar expenditure in watches.
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Best watch brands...
Wilsdorf
Patek Philippe
Becsei
Vacheron Constantin
Loth
Feigenbaum
FP Journe
Breitling
Rolex
Kaiser
TAG Heuer
Chopard
Rollie
Berard
Schneider
Sirmakes
Hayek
Biver
Movado
Breguet
Zenith
Viot
Hess
Dowling
Barrouh
Daniels
Levesque
Miarecki
Kaprielian
Krone
Cartier
Voutilainen
Trapani
Tissot
Tutima
Krone
Kobold
RGM
Montres Allison
Scheufele
Montana
Grand Seiko
Franck Muller
Omega
Cedric Johner
Lederer
Maingot
Levesque
Arabo
Babin
Schneider
Wibmer
Thomke
Thiebaud
Arabo
Babin
Barouh
Becsei
Bennahmias
Berard
Bernheim
Childers
Cinette
Daniels
De Sole
Dowling
Ei8htohms
Feigenbaum
Ficklin
Heiniger
Hess
Kaiser
Kaprielian
Krone
Lederer
Levesque
Lititz
Maingot
Miarecki
Montres Allison
Nataf
Odets
Pennsylvania
Perrin
Perroulaz
Rollie
Scheufele
Schneider
Sirmakes
Thiebaud
Thomke
Trapani
Viot
Voutilainen
Wibmer
Wilsdorf
Zemer
Zenith
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Sure there are many others, but these are very good watches.