I find this to be a very hard decision, every time.
I find if I have the Kindle version I will read the book much faster and am more likely to get it read within a reasonable time frame at all.
That being said, there are plenty of books that I really would prefer "future proof" copies of. It's easy for me to buy fiction in Kindle format, but when it's a book I may want to deal with again one day (David Bohm's "
On Dialogue" for instance) I really have a hard time deciding. Unless there is just a huge price difference.
And still, I really want to be able to read it on my Kindle! AHHHH!