I mainly went with Excel for convenience: with enough time I'm pretty sure I could get GD to do what I needed (manually add & size error-bars, calculate a regression line, manually overlay graphs to add it, etc.). I guess I'll try adding a simple chart and see how Excel responds.

I like the idea of storing the file in the DB, but won't I need to write that data to disk when I want to display it? If I try to embed it in an HTML page, I'll need a static link for that, will I not?