Are there tools available for trimming PDF margins?

Try BRISS. Free, open source and cross-platform. There's a nice discussion of it at the MobileRead forums.

As mentionned in other answer, BRISS is great. Another really handy tool is k2pdfopt (http://www.willus.com/k2pdfopt/). This tool is really great to take a pdf and optimise them for the Kindle (or any device with smaller screen). It works really great for scientific 2 colums paper since it reflow the text while keeping the equation and images.

As was already pointed out k2pdfopt is a great tool.

If you do not mind jailbreaking your Kindle (and possibly voiding your warranty) there is also the option of using this tool directly on your reader. This is implemented by three forks of the same software package:

• Kindle PDF viewer is the original and supports Kindles with Keyboard (designed for Kindle 3).
• Kindle Open Reader supports touch devices (Kindles and newly also Kobo)
• Librerator supports non-touch Kindles (including Kindle 4)

They deal with multiple columns, allow reflow of text and change of font size. They even manage not to destroy scientific formulas and images when reflowing.

At this time there are minor problems like missing spaces between two words of a line jump, but I consider them unproblematic. Maybe they get fixed in one of the next versions.