I really love how Zoho Desk handles email threading, but it can get really hard to distinguish threads from one another after a ticket has been live for a while. For example, you can forward a thread over to another internal member to ask a question and have that simultaneous thread directly next to the original support thread from the customer. When this happens, the forwarded thread becomes private (perfect), but it's just distinguished by a barely visible icon/descriptor. It would be great if private threads could be shaded in a different color (edited image below to show this idea). A great example of this is how Manage Engine displays separate threads as different colors depending on their type (public note, public reply, private note, forward, etc.).

Edited Screenshot of Zoho Desk to Show Shaded Threads:

Manage Engine Threading: