While it is possible (and probably good) to do all the calculations with paper, pencil and calculator, if you deside you want to make one small change to see what effect it would have, your going to have to do it all over again by hand. There are many benefits to rocket design software, but that is probably the best.
Which program is the best? There are two main competetors that I know of:
There are many controls on the main screen of SpaceCAD. At a first glance it is harder to assess how to use the program, but with a little bit of tinkering it becomes apparent.
I have come to think that SpaceCAD's interface is a little more complicated than RockSim's, and it isn't even as powerful. (I may be biased: I really like RockSim). But SpaceCAD is much cheaper than RockSim, and so still might be just as good a deal as - if not better than - RockSim.
SpaceCAD design file
RockSim design file
Also, the simulation results aren't as easy to read in SpaceCAD, but you can do it. RockSim even goes as far as to provide the user with an animation of their rocket's flight profile!
In short, I suggest that SpaceCAD can do most of the things RockSim can do, but RockSim does them better.
-SpaceCAD - $59.90
-RockSim - $108.95