Do you mean that you want to plot the vector field of the system?
In my opinion the better tool for differential equations is Mathematica. For open source packages there is yacas, maxima, sage...
In the following link you may find some informations about plotting ODEs in gnuplot
http://gnuplot.10905.n7.nabble.com/diferential-equation-plotting-td1350.html
The (rather expensive) programs Maple and Mathematica are probably easiest to use. However, with little efforts you can use open source software. Sage (mentioned in Jamal's post) is still a bit more difficult to use than Maple or Mathematica, but - like these - it allows symbolic computation, numerical solutions and graphical representation in a python-like syntax (see below).
Octave (a Matlab clone) allows to solve the ODE and plot a solution, or, to plot a vector fiel, etc.
My preferred solution is to use python, which needs a bit more learning effort, but provides (via the modules NumPy, SciPy) all kinds of numerical methods as well as visualization tools (via the modules Matplotlib, myavi, etc.)
Gnuplot is a good option for 'just plotting', if there is no solving implied. (Gnuplot is a possible 'graphical frontend' for some of the open source solutions.)
IMHO Modelica Language is the best algebraic and differential equations solving platform out there. There are plenty of open source implementations available including OpenModelica and Jmodelica.
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