One theme Stoppard writes about in Rosencrantz and Guildenstern are Dead is the idea that fate is ultimately in control of human life. Because he has chosen two Shakespearean characters as the basis for a new story - their own life details can be added (as Shakespeare left these out) - but their fate of death is sealed - because we know at the end of Hamlet, they die. The play opens with the two characters flipping a coin. This presents the idea of "chance" which is then contrasted with the reality that chance does not in fact control destiny, but something else much stronger does.
Another theme touched on is similar to the "appearance vs. reality" theme present in Hamlet. In this play, as in Hamlet, there are other "players" who perform plays within the play. The theme produced here is the idea that often art (drama) presents a reality that is more realistic than life experience itself. This is one of the more psychological themes that questions existence and purpose.
Finally, death is a subject presented throughout the play. This theme creates a full circle with the two themes. Rosencrantz and Guildenstern frequently discuss the inevitablity of death, the common denial of humans with regard to mortality, and again - the life purpose questions arise as they realize - there is nothing we can do to stop death - so why live?