Depending on what type of diagram I need, I use one of:
1. LaTeX + TikZ - if my diagram is simple or lends itself well to the TikZ syntax, I can usually get it done quickly and have it look professional.
2. Graphviz - if I'm drawing anything that can be represented as a directed graph, Graphiviz is fantastic due to it's automatic positioning and layout.
I second ipe, used it together with LaTeX for my theses. It looks great, gives you many options while being an easy-to-use WYSIWYG tool and integrates with LaTeX typesetting (you can typeset in the diagram). The PDF export makes it also usable in other contexts.
1. LaTeX + TikZ - if my diagram is simple or lends itself well to the TikZ syntax, I can usually get it done quickly and have it look professional.
2. Graphviz - if I'm drawing anything that can be represented as a directed graph, Graphiviz is fantastic due to it's automatic positioning and layout.
3. ipe (http://ipe.otfried.org/) - for heavy lifting where neither of the above will cut it, ipe does a great job. It's basically xfig, but on steroids and with a modern UI. Here are some samples: https://github.com/otfried/ipe-wiki/wiki/Showcase