If it's a token that's going to be used regularly (ie: your company address, LinkedIn profile, etc), you would put that in the highest folder available so it trickles down to all of your Programs. I've created a "Universal" folder that houses everything for this purpose and it works great - we just moved offices and I only had to change our address in one place because all my templates are tokenized.
Tokens that are specific to a Program (ie: article text, header image, etc) are best created, then, at the Program level.
Edward Unthank has a really good post about using tokens here: Marketo Tokens: Ins and Outs
He also had an amazing session at Summit 2015, where I basically stole the idea for a Universal folder. Definitely worth checking out: Sessions – The Marketing Nation Summit, April 13-15, 2015 – Marketo