We just added support for Piwik to Virtualmin. It's got a little while to go before it's a match for Google Analytics, but it makes great use of the latest in Open Source tools (like Open Flash Chart, which is a nice charting library)...and it still has the "needs a JavaScript bug" negative, though, realistically, there's no way to get all the data without one...but if you use more than one analytics package you end up spending a lot of time loading JS bugs on first visit.
I think I'd generally prefer locally generating my analytics reports. All that data has value (otherwise Google wouldn't want it so badly), and it probably has more value if it only belongs to me, though I may not be sure exactly how to make use of it.