I don't think Descarte's philosophical phrase would have the same effect if he had said "Je pense, alors je suis"...I think, so I am. Donc is more formal and has the meaning of therefore, which Damien expressed in terms of a logical deduction or the result of a hypothesis and conclusion. Alors is a bit more conversational and less "heavy".
For example, I explain a problem to you and you can suggest...Alors, qu'est-ce qu'on va faire? So, what are we going to do (about this)? Or you could be more decisive and proactive and incite me by asking Donc, qu'est-ce qu'on va faire? Therefore, what are we going to do (about this)?
Even by itself you can ask someone: Et donc? And...what's your point? Why should I care?
Et alors?...So what?...what's the matter? What does that change?
But it all really depends on the context and intonation of the speaker.