Sometimes I don't want to flight from one place to another directly, but do some stops. I'd like to select all the cities to fight through. And select connection time, airline, etc.. if possible.
Is there well-know websites that allow it?
matrix allows you to specify almost any conveivable trip combination. You can specify the cities or airports to fly through, the layover times, the airline alliance or airlines and even the aircraft that you're willing to fly.
Example: If you wish to fly from London to San Francisco via New York with a stopover in New York of more than 48 hours on the outbound, only on aircraft operated by American Airlines, you would use LON::O:AA*/minconnect 2880 to SFO::O:AA*
If you'd like to further specify your requirements, I'm sure we could supply you with the options you would need to use.