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I was recently looking for a javascript charting library and I evaluated a whole bunch before finally settling on jqplot which fit my requirements very well. As Jean Vincent's answer mentioned you are really choosing between canvas based and svg based solution.
To my mind the major pros and cons were as follows. The SVG based solutions like Raphael (and offshoots) are great if you want to construct highly dynamic/interactive charts. Or if you charting requirements are very much outside the norm (e.g. you want to create some sort of hybrid chart or you've come up with a new visualization that no-one else has thought of yet). The downside is the learning curve and the amount of code you will have to write. You won't be banging out charts in a few minutes, be prepared to invest some real learning time and then to write a goodly amount of code to produce a relatively simple chart.
If your charting requirements are reasonably standard, e.g. you want some line or bar graphs or perhaps a pie chart or two, with limited interactivity, then it is worth looking at canvas based solutions. There will be hardly any learning curve, you'll be able to get basic charts going within a few minutes, you won't need to write a lot of code, a few lines of basic javascript/jquery will be all you need. Of course you will only be able to produce the specific types of charts that the library supports, usually limited to various flavors of line, bar, pie. The interactivity choices will be extremely limited, that is to say non-existent for many of the libraries out there, although some limited hover effects are possible with the better ones.
I went with JQplot which is a canvas based solution since I only really needed some standard types of charts. From my research and playing around with the various choices I found it to be reasonably full-featured (if you're only