Pushed to master, commit 7074c5

This should at least be configurable somehow, or it will make Geary useless for some workflows. 
For example: 
To reduce the noise in my inbox, I filter all mails that come from different development related mailing lists. Some lists are high traffic and some are low traffic. For high traffic lists, I guess the unread count is less important since these folders will have unread mails quite often. However, for the filtered mail to folders with low to medium traffic it is good information to have a badge. 

But the mailinglists are not the most important workflow it breaks. I also tend to sort mails based on different subjects that are important to me, so they will not drown in the noise that still exists in my main inbox. It can be mails related to my boat (different mails from my marina and things like that), different projects (like building a new house) aso. These are quite important mails, they may contain mails in need for immediate actions (like paying a bill, signing and returning important documents aso). Not having a badge showing that a new mail has arrived in these mailboxes, defeats the whole idea why they were sorted to begin with.

Removing badges from other folders than inboxes, is based on the idea that filtering is done to archive or that it is less important mails that are filtered. I claim that there are probably equally many workflows where the Inbox is the less important folder and the important mails are filtered. 

Hence, if unread count badges are removed it should be configurable and they should still be shown by default (to follow the principle of least surprise).

There's a difference between unread email and new email, and that's what this ticket was originally addressing.

There is a ticket to indicate new email in all folders (bug #714655), which it sounds like would solve the issues you're describing.