In gmail, I use the 'star' function to mark emails that I need to follow up with. More often than not, I can usually look at the subject line and sender and see if it's something I'll need to reply to, or whether I will need to do something (like an invoice that needs paid, or an email from a friend). If I still need to do something with it, whether I've read it or not, I star it. When I get free time and browse to my email, I'll be reminded I need to do stuff and finish it up. This works because I get a fairly low volume of email. Your experience may vary, especially if you get a lot of stuff to respond to.

You can use the Zero Mailbox approach. Google for it. You will get loads of material.

"""I have a hard time making sure I reply to every single email where a reply is needed. I tend not to reply emails when I'm programming and "in the zone", therefore I often have to wait before replying."""

And what's the problem with setting 1-2 hours when you are off-the-zone to batch reply to the accumulated emails?

"""to make sure I reply every single email on time ?"""

On time doesn't have to mean "immediately". Same day is fine.