Email gone missing? A message that was sent did not arrive? Consider the following scenarios.
In the same way that people who change employers can have superannuation funds in accounts they later lose track of, it's now quite common for internet users moving between service providers to lose track of old email accounts and to have new email accounts they are not aware of.
Email is an increasingly critical business tool and any organisation who has changed ISP, or had staff leave may have mailboxes quietly accumulating messages which nobody sees. It's worth undertaking a review of your email to ensure these messages are being downloaded, and you should start with the mailboxes provided by your internet provider and web/domain-hosting provider (as the case may be). It's also worth checking you don’t publicise an email address that doesn't work! It's amazing how many businesses publish obsolete email addresses on their websites.
If you have a domain name, most hosting providers have a “stray mail” mailbox to hold all the badly-addressed incoming email instead of issuing a failure notification. (Try sending yourself a message with the address spelt wrong and see where it turns up.) In some circumstances, this can be very handy, but if you don't know about it, you may be ignoring messages and the senders won't know the message didn't arrive.
But using stray mail is not really a good idea. A few years go, spammers realised they can send messages to domains without knowing any real addresses. If you have a domain name and are plagued by spam, you may notice that a lot of it is addressed nonsensically. Ask your hosting provider about disabling stray mail.
Many ISPs are now automatically applying spam filtering. This is supposed to keep spam out of your Inbox so you don't even need to download it. However, generally they don't tell you what's been filtered and you still need to regularly check the “Quarantine” folder by logging in to your mailbox on the web. Furthermore, many ISPs started doing this without any warnings or announcements so you may not know when or if it started. The upshot is you may have legitimate mail being quarantined in error (“false positives”), you won't know it's there and the sender won't know it didn't reach you → CHAOS.
Some people don't care much about their email, but for many businesses it is mission-critical and they can't tolerate email that vanishes. Thus we generally suggest ISP filtering be disabled, so all your email is delivered and you can make a choice about what's spam and what isn't. Of course the downside is that you'll get more spam, but spam filtering is not perfect, and most likely will never be good enough that you can immediately delete it without looking at it. Spammers have shown over many years that they can defeat filtering either with new techniques or the plain brute force of volume. That's not to say spam filtering is pointless, but it should be done on your computer and not upstream at the provider.
See also SBS 2008: Recovering Quarantined Email.
When employees leave, it's common for their email address to be deleted. It's not a bad idea to keep your email directory neat and tidy. But just because someone leaves, it doesn't mean their job function has ceased, or that they don't have suppliers and customers sending them messages. If you quickly delete someone's account you may have important communications from business partners being rejected, and because rejections can be misinterpreted by the sender as spam, neither party realises the message didn't get through. Sometimes you'll be lucky and the sender will contact you for updated details, but not always.
Thus the best action is to keep the mailbox active but redirect it to an appropriate person. Don't simply add a generic “this-address-is-no-longer-monitored” message. Notify as many people as possible that the address has changed. And then in some period of time, say a year, you can remove the mailbox.
Most hosting providers have alias or forwarding options, and usually provide more mailbox capacity than you could ever use, so you don't have to worry about overloading the system with obsolete addresses. It's much better to maintain continuity of addresses.
Email Client Filtering/Views
Sometimes email arrives but you can't find it, so you assume it's gone or didn't arrive in the first place. There are several reasons this might happen.
When using Microsoft Outlook with an Exchange mailbox in cached mode, not all messages appear in some some folders. However, with Outlook in non-cached mode, or using Outlook Web Access, the messages appear.
This may occur if the folder is damaged or corrupt. To correct, open Outlook in non-cached mode. Rename the folder in question, and create a new folder of the same name. Then move the messages from one folder to the other. Wait a moment while the changes take place. Close Outlook, re-enable cached mode, and open Outlook. Outlook will take a few moments to synchronise the local cache against the Exchange store and the messages should appear properly.
If your mailbox has been compromised, malicious third-parties may be deleting email before it arrives. If you have reason to suspect this, change the passwords for all mailboxes and be sure to use complex and unique passwords.
Invalid MX Records
Your domain's MX records tell senders' email servers where to route email addressed to you. But if those MX are correct, but too complex, some servers may refuse to resolve them properly, with the result most email arrives correctly, but some doesn't. Check out Troubleshooting 5.4.4 Email Errors.