Since nobody has mentioned it yet, KOReader is an open source reader application for ereaders, kindles & others, and has the ability to reflow PDF's. While not perfect, it can work good enough to read well formatted PDF's.
The technical detail about latest WatchThis hasn't been published yet, but the previous KindleBrake seems to be using malicious JXR image payload via built-in browser. That sounds like pretty serious security flaw to me.
Kindles need to be jailbroken to use koreader, and Amazon apparantly makes that harder with each device :-/
I have this as a right-click action for files matching *.pdf in my file browser (thunar):
So if I right-click on a pdf I can immediately reflow it into a kindle-readable version.(%F is the quoted file name, in your terminal you would `k2pdfopt -ui- -dev kp3 'something.pdf'`)