(FORTUNE Magazine) – Feeling overwhelmed by e-mail? Just plain annoyed? You're not alone. Internet mail may have become a valuable business tool, but your inbox is probably cluttered with unsolicited messages, sales pitches, and annoying discussions that were once limited to the water cooler. You can't slam your door to shut out all the nonsense, but many of the popular e-mail programs have tools to help you manage the rising tide of paperless correspondence.

I will focus on two of the most widely used: Outlook Express, which comes as part of Windows 95 or 98 (or Office 98 on the Mac) and Qualcomm's Eudora, which has both a shareware version and a more elaborate commercial edition, Eudora Pro. Other popular e-mail "clients" include Netscape Mail, which is built into Netscape's browser, and on the Mac side, Quickmail. While Web-based mail can be useful for checking your messages on the road (see The Dreyfuss Report, Oct. 11, in the fortune.com archive), PC-based mail is a lot more secure for business use and offers more options.

Back to Microsoft. I have to admit that Outlook Express is among the rare Microsoft products that work well in their first iteration. Don't confuse Outlook Express with Outlook, a bloated Microsoft product (part of the Microsoft Office suite for Windows) that does calendars, meeting notes, and other desktop tasks as well as e-mail. Express handles Internet mail (known as POP3) and mail based on the newer IMAP standard that many companies are adopting. Like other e-mail software, Outlook Express collects mail from several different accounts, so that you can consolidate and manage all your messages.

But getting the mail is just the first step. Sorting the digital wheat from the chaff is the key to using your time better. The filtering tools in e-mail are variously labeled rules or filters or inbox assistant. Whatever their nomenclature, it is worth investing the 20 to 30 minutes it takes to learn to use them.

Both Outlook Express and Eudora have tried to make the process as simple as possible. Eudora Pro lets you pick a message as an example and apply several preset rules to it. You could, for instance, create a rule that moves any incoming message not addressed specifically to you to a junk mail folder. This will reroute much of the Internet spam, which often uses fake names or mailing list names. I prefer not to send these messages directly to the trash just in case an important message from the boss gets dumped.

Filters can also flag important messages, setting up, for example, a rule that sends any mail from your boss to a special MAIL FROM THE BOSS folder. Some programs will even let you change the color of the message title, to make sure you don't overlook it. You can create rules to automatically move messages with certain topics or key words into special folders. You can ship mail from annoying correspondents directly to the trash. And you can also send automatic responses; for example, you can set up a rule that responds to all new e-mail with a message that you're on vacation.

The biggest advance in e-mail in the last couple of years is in the way it looks. The HTML codes used for Web pages have worked their way into e-mail. The newer e-mail products handle these messages well, showing them in all their glory, complete with eye-straining fonts, ad banners, and color flashes. Some of these products offer templates, so that you can send your own eye-straining mail and not feel left out of the design frenzy.

HTML mail provides an opportunity to send lively messages to your customer, but remember that a simple message with substantive content beats out a fancy pulsating billboard of no relevance. Otherwise you too may end up moved directly to the trash without ever being seen.