The best replacement for gnuplot is grace.

The best alternatives to gnuplot are rated as following:
★★★★★  grace
★★★★★  octave
★★★★  fltk
★★★  pgfplots
★★  plotutils
★★  xmgrace
★★  gnu octave
★★  matlab plot
★  plplot
★  qtiplot
★  rrdtool
  mathgl
  matplotlib

Your alternative for gnuplot is not listed? Suggest!
Speaking about gnuplot, one probably shouldn't forget about error bars.

Other search terms related to gnuplot and their ratings are:
★★★★★ error bars
★★★★ dots
★★★ linespoints
★ octave
tics
datafile
You have in mind a companion for gnuplot and it is not yet here? Propose!



Google Trends

Scale is based on the average worldwide traffic of gnuplot in all years. Click on graph for more.
gnuplot
grace
octave