Glad to hear that you have found my earlier Gmail articles of benefit. I too have dozens of filters and dozens of labels to help automatically organize and manage my incoming mail stream. Well, flood, now that we're talking about it. The key article if you want to get started taming your own Gmail mailbox is probably this one: Use Gmail Labels, Folders and Filters to Manage your Email.

Problem is, it seems like the labels/filters are designed for a relatively small number and that once you get a bunch of them, those labels that don't start with "A", "B" or "C" end up off the screen, making it really hard to see if they have unread messages!

Fortunately the Gmail team has encountered this problem and there's a way you can mark a given label folder (aww heck, let's just call them "folders" and not worry about the fact that Google doesn't like that term for them!) so that it only appears on the list if it has new messages within. Otherwise, it's neatly hidden behind the scenes.

Here's a subset of the folders I have in Google Mail, each tied to one or more mail filters:

I get a lot of notifications from Facebook so I push them into their own folder through use of a couple of different filters, as you can see. I also, however, automatically mark most of them as read so it's rare I need to peek into the folder to see what's going on. A perfect guinea pig for what we want to accomplish!

The secret is to move your cursor over the colored box adjacent to the particular label, then click once the downward triangle appears. A menu of options appears:

Here's where you can change the label color, but let's stay focused. Note the second block: "In label list" you can set this particular label to show, show if unread or hide. It's the middle option that is what we want to select, so I'll do that, marking this particular label "Show if unread".

Instantly it vanishes from the list because there are no unread messages:

When an unread message appears in the folder, however, it reappears in bold and with an unread message indicator:

That's all there is to it. Just mark all of your infrequently used Gmail folders as "show if unread" and you'll find that you've tamed the beast quickly and easily.

Before we go, one additional tip: if you want to move into a folder while it's hidden, just use the handy "More" entry at the bottom of the list:

You can see that it lists every single label I have in use, regardless of they're hidden, only showing if there's new mail or showing all the time. Handy!