Here are a few suggestions based on one key premise - the inbox shouldn't be storage, it should be an inbox - where emails come in and you are able to quickly deal with them or dispatch them to some other mechanism where they will be dealth with, but most importantly they are removed from the inbox fairly quickly.
If you are using IMAP to access your gmail you won't be able to use some of these. If you are serious about keeping email organized and manageable, I have yet to find an IMAP client that can keep up with the abilities of the web interface.
Start using filters to unclutter the inbox. For example, if you receive recurring bill reminders or payment confirmations from your utility, internet provider, etc., create filters for these. There is no need for these to be in your inbox - once they are filtered and labeled, you will always know where they are when you need them.
Enable priority inbox.
Stratifies your inbox and highlights the most important emails first.
Consider GTD methodology.
The way this works for me is when I check email (I don't "get" emails, I check email, i.e. don't have it always on which is a major distraction), I either deal with an email right away (if it takes less than X minutes, where X should be 5 or less), or it goes on a list/calendar to be dealt with later. The key is to archive the email regardless of what you do. Why? Because you've either taken care of it or its somewhere else where it will be taken care of; it no longer needs to sit in your inbox.
Enable Send and Archive.
This makes #3 easier where dealing with an email involves replying. Adds a button that both sends and archives the email, making it that much easier.
Check out Boomerang for Gmail.
I don't use many gmail extensions/plugins, but this is one. In essence it handles archiving and then unarchiving an email with very slick options for scheduling. Why is this useful? Sometimes I really just want an email to be gone (clean inbox), but don't have the mental energy or time to either deal with it or move it to a list/calendar. This can also be useful to unarchive sent emails, particularly for people who you know will let emails fall through the cracks. Emails that are "boomeranged" end up in your inbox again, when you specificy, marked as unread.
I'll update this as I think of some more tools/tricks I use.