Inspired by this conversation, I hacked up this functional comment link:

http://kitchingroup.cheme.cmu.edu/blog/2015/04/24/Commenting-in-org-files/

It has a custom link type that exports in html and latex, and when you click on it, it asks if you want to delete the comment. 

John

-----------------------------------
Professor John Kitchin 
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803

On Fri, Apr 24, 2015 at 5:38 PM, Vikas Rawal <vikaslists@agrarianresearch.org> wrote:
>
> [...]
>
>> Why use footnotes when you can use todonotes?
>
> Good question!
>
> It's personal preference: I prefer footnotes as I am often using narrow
> margins and anything more than a boxed footnote number is too
> much...  However, it is trivial to change the export template to use
> todonotes if that's what Vikas prefers.
>
> The key message I was trying to get across is the use inlinetasks to
> leverage the capabilities of org for TODO management.
>


Thanks all. It has been lovely to see all the various solutions on offer. I thought I was posting a lame query, and was feeling a little sheepish when I first sent it. But it has been nice to see these various approaches, with their little ingenuities.

Wonderful org friends, thank you once again.

Vikas