There are some nice answers by folks here-
However specifically for 'learning by projects'-
Make a simple page where you change color of background etc on clicks
Make a calculator
Make a Todo app (store data on localstorage, use simple javascript or jquery)
Make a simple chrome extension to customize your homepage (or anything)
Make a small game ( Eloquent JavaScript walks through making a game)
Make a small Express based app (maybe your dynamic personal website)
Finally choose any of these new JS frameworks and make whatever you wish.
I will recommend that you use Eloquent JavaScript as guide for learning theory part while learning it.
Good luck, build something and show us on Hashnode. :)