At the present time, the vast majority of high grade mechanical watches are equipped with automatic movements. The hand wound mechanical movement represents a relatively small % of most companies' total production. For example, well over 90% of Rolex watches are automatics. The Rolex Cellini models are manual winds. Patek Philippe and Vacheron Constantin still make a significant number of hand wound movements. The Patek 215 for example is still made and is used in a number of basic Patek Philippe watches including the 5196 and 5119 Calatrava models. Interestingly, Patek recently discontinued its ultra-thin manual wind 3520 model which was equipped with the caliber 177 movement which was not a Patek-designed movement.
Vacheron still makes watches equipped with its ultra-thin 1003 manual wind movement. Additionally, Breguet, Blancpain, A. Lange, and even IWC, Zenith, Omega (the classic Speedmaster Professional) and Panerai make manual wind watches. Other companies like Breitling seem to have virtually abandoned the manual wind movement for movements equipped with automatic winding systems. Although the original Navitimer and Cosmonaut were manual wind.
As to which is better, there is no answer. Many of the best watches in the world are manual winds including most minute repeaters and toubillons and many high end chronographs including Patek Philippe's 3970, 5970 and 5004 perpetual calendar chronographs as well as Vacheron's Patrimony Traditionnelle Chronograph model 47192 as well as the ultra complicated Patrimony Traditionnelle Calibre 2755 which includes both tourbillon and minute repeater complications.
Interestingly, other than Rolex, the majority of women's high end watches are equipped with quartz movements. Patek Philippe's production is about 25% quartz movements and virtually all of these are for women's watches including the ladies' Nautilus and Twenty-Four models.