What is the best way to run HTTPS for drupal commerce I have seen the module Secure Pages, and also found Custom SSL redirect and read all the issues related to this and Commerce, but most seem out dated.

Can anyone say as of this point what is the best way to run the site on http and the checkout (anonymous users) with https?
It's hard to say what's 'best', it depends what you mean by that.

If you're just looking for a working solution, the dev version of Secure Pages along with the core patches it recommends works great. 

Best thing you can do is install the various options you've identified, do your testing as normal, and ask a more specific question if the modules do something you don't expect.