Not sure what gliffy is but Graphviz can conceptually draw the same thing. You can have box shapes and colors for nodes and edges both. However, the rendering layout itself is usually unpleasant. You can have some control but it's really suboptimal. As I said, Graphviz is both simple and very powerful so no reason to not use it to represent data in concept.
Plus it goes in your VCS.
Gliffy[1][2] is a web app for drawing diagrams and schematics of various kinds. You get a large library of shapes - most of UML, classic flowchart, some UI mockups, swimlanes, now also the root of a mindmap - and a few tools for connecting these shapes to each other; the connections are real connections, not lines, ie. they follow after the shape if you move it, and they know when they intersect and can render a "hop" where needed. You get a lot of freedom in styling the diagrams (change color, thickness, a curvature of lines and color, background, font, font size, etc. for boxes and text), and the UI is not that bad. It, however, seems to have some performance issues, because after a certain size the experience degrades and you need to reload the page every now and then.
I know and like pure-text diagramming solutions, but they don't work that well for diagrams designed to span multiple displays in width or height. Or put another way - my editor, as glorious as it is, is not designed for rapid zoom-in/zoom-out on various parts of an 80000x80000 rows/cols text file. I want to be able to work in an interactive environment, where I can rapidly switch between the overall outline view and the focused, detailed view of just a few nodes. Moreover, I need to able to embed (and preview if possible) different kinds of content, from syntax-highlighted text to images to videos, plus it should render natively in a browser (hence the SVG).
My use case for this is putting together a knowledge-base (think Wikipedia, just for my personal data), which would use direction, color, line thickness and kind (dotted, dashed, etc.) to bind related subjects and show the relations between them in 2 dimensions. Feature-wise Gliffy is close to what I have in mind, but it doesn't handle a scale big enough to be called a "knowledge-base" - "infographic" is the most it can produce.
