Converting PDF eBooks into a Kindle format

Over the past couple of years I've amassed quite a collection of guides, tutorials and ebooks in PDF format. A lot of these are quite useful for work, especially PDF documentation, and rather than have to be at a computer every time I want to read how to do something in Sitecore or to read through a software testing ebook I'd like to do it on my brand-spanking-new Kindle.

However, even though there is now a native PDF reader on the Kindle due to the nature of PDF's they are practically unreadable. The text doesn't wrap due to how PDF's are sized and so far after a bunch of Google searches I've yet to find a viable solution to get my PDF's converted into a readable Kindle format.

Sometimes these books have code or pictures/tables in them, but most of the time they're text-heavy and to be honest I'd be surprised if there wasn't a free tool to handle the converting of PDF to one of the (seemingly many) Kindle formats.

So, can anyone help me out with this?

EDIT: I've tried Calibre, and have checked their forums to play with some of the advanced settings, yet the solutions available seem to be extremely poor, especially if the book you're attempting to read contains equations, code, or anything outside of plain text.

I've also tried Amazon's conversion service, which wasn't much help with such documents. The best way I have found so far is to build the entire thing over again in ePub or RTF format and convert to MOBI from there. This works for text-heavy books with tables, but anything technical still isn't covered.

Can anyone help with this?