following the discussion here on stacking algorithms and implicit resampling, I wonder if anyone here has some experience with the stacking software Swarp
It's from the same author as SourceEXtractor and Scamp, and it's written with photometry precision in mind. It has tons of options that allow you to fine-tune the method used for stacking and it's command line oriented, so great for automatic processing. I haven't tried it yet, as far as I understand it requires that the input frames are plate solved (which could be done by the tool scamp by the same author, for example, also in batch mode).
So for those who have Linux, this could be worth trying I guess if you mistrust the photometric fidelity of your favorite stacking software.