The best replacement for graphviz is gephi.

The best alternatives to graphviz are rated as following:
★★★★★  gephi
★★★★  gnuplot
★★★  yed
★★  tikz
★★  networkx
★  dia

Your alternative for graphviz is not listed? Suggest!
Speaking about graphviz, one probably shouldn't forget about doxygen.

Other search terms related to graphviz and their ratings are:
★★★★★ doxygen
You have in mind a companion for graphviz and it is not yet here? Propose!



Google Trends

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