I have a kindle dx for the sole purpose of reading physics papers. Overall, I've found that the support for math equations in pdfs is very good, with one notable exception. Overall it handles the equations in pdfs really well- pretty much it'll appear the same way as it does on the computer screen. The only thing I've found is that for pdfs compiled with pdflatex, the letter beta is printed over top of the previous letter. This happens on all ereaders using a pdf viewer based on adobe's toolkit- including the nook and sony ereaders. However, if you can get the latex code, you can work around this by compiling to postscript and then converting to pdf. (For all the papers on the arxiv, you can get the latex code.) With that one caveat, though, I've found that the display of math equations is great.
One other thing, though- it doesn't support hyperlinks in pdfs. If you're reading long pdfs (from summer schools or such), it can be difficult to navigate. But, except for the letter beta, equation support in pdfs is very good.