So I was considering GIMP, LaTeXDraw, Inkscape, Xfig, GraphViz – and in a weak and confused movement FSLView – to draw a graph. Then I saw Dia, installed it, and I found it quite suitable. The arrows attach well to the objects and it has a range of output formats.
The unfinished graph displays neuroinformatics databases and web-linkable identifiers between them: My Brede Wiki and Brede Database along with fMRIDC, OpenfMRI, Cognitive Atlas, CogPO, IBVD, SumsDB, BODB, CoCoMac and the more general PubMed.
There is an arrow from PubMed to the Brede Database. That is because someone (not me) apparently has defined LinkOut for the Brede Database. Thank you.