I don't actually know many protest songs, except the ones already mentioned - but I've just written one myself so I guess I could call it my favorite (though biased!).
I'll be posting it as a Hub soon, but here's a sample of the lyrics:
...make some noise, for a silenced voice,
For the weak who long for their word,
For the ones who cry, beaten down by lies,
For the ones without rights to be heard...
...Worlds go round, but the trumpets sound
For ears that are tuned to the times,
For an equal chance, for all who dance,
With freedom scratched on the signs...