For reference, these are the places the transactional e-mails can be adjusted:

General:
Currency Setup – Scheduled Import Settings
* Contacts – Email Options

Catalog:
Catalog – Product Alerts
Google Sitemap – Generation Settings
* Email to a Friend – Email templates

Customers:
* Newsletter – Subscription Options
* Customer Configuration – Create New Account Options
* Wishlist – Share options

Sales:
* Sales Emails – Order
* Sales Emails – Order Comments
* Sales Emails – Invoice
* Sales Emails – Invoice Comments
* Sales Emails – Shipment
* Sales Emails – Shipment Comments
* Sales Emails – Credit Memo
* Sales Emails – Credit Memo Comments
Checkout – Payment Failed Emails

Advanced:
Admin – Admin User Emails
System – Log Cleaning

(* Per storeview/language)