I would also like to suggest an app called the HelpCenter App. The reason it works best with Shopify is simple - it's designed for Shopify and its' merchants in mind. Besides some must have helpdesk features (combining inboxes to one platform, tags, auto-replies, etc.) it also enables customer support team to have an instant overview of customers' previous inquiry and purchase history. This helps to boost customer experience as the support is more personal.
HelpCenter App's helpdesk is also suitable for anyone just starting their online store. The free plan includes 50 helpdesk tickets in a month.
Moreover, the app also comes with three other features - FAQ builder, live chat and product description tags.