It depends on the context. You can use "a través de" for instance in this sentence " Puedo ver a través de la ventana" (I can see through the window), but you cannot say "Puedo ver por medio de la ventana".
You can use both phrases in the case you mean "by means of".
"a lo largo de" you can use for making refer of time, relationships, distance.
I hope this helps, if you need further explanation or examples, just ask.