You need to research each plant to see which type of propagation is recommended. Your question asks what we prefer to root but there are way too many plants to get one answer. ?Maybe narrow the question to one or two types of plants and make a post on the propagation forum?
There is a search box here on NGA. From the home page type into the search box and look for articles and posts already here on NGA.
Typing just the word "propagation" gets this result:
http://garden.org/search/index...
Vary your search words to find more results:
rooting in water
rooting plants
propagate in water
etc.
My all time favorite method to root just about anything is the Forsythe Pot method. Lots of good information here on NGA and on the internet. I've had success with everything I tried including Gardenia and Mandevilla.