For high-level UML charting, I'm about to start looking into UMLGraph. It completely supports UML and its output is the input to GraphVis, another tool which is really useful.

Speaking of GraphVis, I just started it as a way to do some medium-level graphing. You provide an easily modified text description of the system you're charting and GraphVis places and draws the boxes, circles, and arrows. It generates several forms of output including svg, png, and (for those of you who, like me, use a Wiki or web page for distribution) image maps.

I had been using InkScape but that's pretty low-level and requires a lot of effort to change diagrams. I tried Dia but I didn't like the quality or modifiability of the output.

Update: Oh, all these tools are free.

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