Is there any libraries to visualizate simple dependency graphs? I suppose that SVG is good solution.
I'm not sure about PHP libraries, but there's the tool called Graphviz which can be invoked from your PHP code and produce .SVG visialization of your graph.
I used http://www.aditus.nu/jpgraph/ for drawing simple graphs.
ChartDirector is the best, and it has a lot of flavors thus has versions for PHP/ASP/COM/VB/.NET/JSP/Java/ColdFusion/Perl/Python/Ruby/C++.
By learning one, you then be able to use in many programming languages.
I really like Google Chart API: http://code.google.com/intl/fr/apis/chart/
Really simple to implement and there are quite a lot of graph styles.
The if you mean graphs like in "dependency graph", then Graphviz should be mentioned.
Checkout http://thejit.org/