Well, I'm not using *nix, so I can't help you as to where to put the cronjob. But, in a nutshell it's as easy as getting the correct incantation of epub-convert: Say you want to download the NY Times. You'd then have a look in the recipes (found in resources/recipes in the Calibre root) and find the corresponding recipe to be called nytimes.recipe, so you'd get your command to invoke as
Code:
ebook-convert <calibreroot>/resources/recipes/nytimes.recipe todays_nytimes.mobi
which should create a file called todays_nytimes.mobi containing, well, the NY Times articles as of the time you called the command. (<calibreroot> needs to be filled out to be the place the calibre directory resides in your system, see above comment about not using a *nix OS.)
As for emailing said MOBI-file to your Kindle, there should be console programs on a Linux system that can do exactly that, but you'd have to wait for one of the Linux gurus to arrive for an answer. I'd like to point out, though, that, if you have the Kindle with WiFi, you should also be able to add the MOBI file to your calibre library and download it via the content server.