Public transportation works pretty well in prague. You can look up connections on http://194.213.60.4/idos/ConnForm.aspx?tt=pid&cl=E5. Trams and buses run through the whole night, but different lines are active during the night!

If you feel like taking a taxi, you should call one of the bigger operators like AAA (+420 222 333 222) or speedcars (+420 224 234 234).

Useful link about Prague taxis: http://www.praguetaxi.co.uk/