I wouldn't call myself "experienced", as I used Qwt only for a few months, and QCustomPlot for a few weeks. That being said, my impressions are:
- QCustomPlot seems to be more actively developed at present. Last release was in August 2012 (whereas last release of Qwt dates back to 2011). Subjectively, its interface seems more 'aligned' with Qt framework.
- Qwt, on the other hand, seems more mature and featureful. For instance, current release of QCustomPlot has no straightforward way to set the colour background for the axis rectangle (only setting background to a user-supplied pixmap is supported). Another example - Qwt has special classes and methods to facilitate plotting and zooming in-out the curves with a very large number of points. I found nothing like that in QCustomPlot.
EDIT: Author of QCustomPlot is aware of missing functionality to set plot background and promises to add it in upcoming release.
There's also another important difference between QCustomPlot and Qwt - licensing.
- Qwt is LGPL, so you can link it into non-GPL project. QCustomPlot is GPL v.3, which many people (myself included) find WAY too restrictive. QCustomPlot author invites to contact him if you want LGPL license.
EDIT2 (25 March 2013): New releases of Qwt branches 5.* and 6.* appeared in November, which annuls "more actively developed" advantage of QCustomplot
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