I generally use the stock pdf viewer of kindle 3.2.1 on my kindle DXG. The main reason i prefer this over the stock 2.5.8 pdf viewer is the contrast selection. You can increase the black level which makes a lot of pdfs readable. Also you can use the dictionary and take annotations on the 3.2.1 pdf viewer unlike the 2.5.8 one.
I mainly use the duokan pdf viewer for its two column viewer. Also now duokan has a manual pdf crop option which you can specify the margins around the text, and it zooms to the area you specified. This option seems like the answer to your problem (wide margins problem)
But in general duokan seems to not render pdfs (especially the ones with tables and graphics) as good as the stock pdf viewer. So unless i have a specific need for two column view, or the pdf has wide margins i stick to the 3.2.1 pdf viewer.
As far as i know there isn't an alternative pdf viewer except duokan out there. So there isn't much choice for now.
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