pH uses labview, which is a really cool program for data aquistion. You can program in things like digital filters to remove 60Hz noise from your readings. The downside is it takes some getting used to, and you need an ADC and instruments to use it with.
The next best thing I've found is Excel, which is fairly good for plotting and trendlines. Not to mention its very simple.
Finally Cathar recommended Perl w/ GD::Graph which is handy since you can write your own parsers, but if you're not into programming it'll be much more difficult then Excel.
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