First, what are the key differences between POP3 and IMAP?

POP3 is a transfer tool
POP3 is really an email transfer protocol.  Think of it as downloading messages from the server and moving them to your PC.  They are initially stored on the server, then your email software downloads them locally to your computer and removes them from the server.  Now only your PC has your email messages.  Any new messages will arrive at the server and wait for your PC to pick up and move the next batch.  With POP3, your “inbox” is effectively stored on your computer.  That typically means that only one computer can be used to manage your email, and you can even work with your email messages while you’re offline.

IMAP is like a looking glass
IMAP is different from POP3 in that it lets you look at your inbox on the server.  All of your interactions are done live over an active Internet connection, and you manage your messages as they exist on the server itself.  The benefit is that you can then manage your email from multiple computers since the messages are maintained on the server and not pulled down to any one computer as with POP3.  It does require an Internet connection, however.  So offline email management is not possible. Today, with always-on broadband access, this is usually not a concern.

I do email from one computer only
POP3 is perfect for you.  As your computer picks up email from the server, it is then stored on your computer and removed from the server.  Only one copy of your email exists then on your computer.

I sometimes do email from two computers (e.g., workstation and laptop)
POP3 at both computers might be right for you, provided your configure your email software to leave messages on the server after they are transferred.  That way, you can get the same email on both computers.  This puts the responsibility on you to manually delete and remove messages on the server, otherwise they may continue to be stored there forever.  If one of the computers is your primary email workstation and the the other is for occasional checking for new messages (e.g., a laptop while traveling or at home after work hours) then your primary email computer can automatically remove messages from the server after transferring, but your secondary should leave messages on the server.  In this way, you can go back to the primary computer (e.g., at the office) and download the messages you might have already seen when you were on your laptop.

I do email from two or more computers (e.g., PC and mobile phone)
You’re an IMAP candidate. This includes anyone who also does email from their mobile phone (yes, that’s a computer, too).  It is especially important that if you are an IMAP candidate that all of your email account settings on all PCs and mobile phones are set up to use IMAP.  If any one of them uses POP3, you’re going to have problems unless you configure the POP3 account to leave messages on the server.  Even still, then, you might as well use IMAP.

Known issues and warnings
Taking a line from the movie Ghostbusters, don’t cross the streams.  Mixing POP3 and IMAP between computers and phones while accessing the same mailbox can sometimes cause a conflict that renders the server’s inbox inoperable, requiring your email service provider to reset it for you.  Bottom line: use IMAP always on all systems when you check mail from multiple devices.

Outlook is a poor IMAP client. Unfortunately, with the ability to easily synchronize contacts, calendars, tasks, and notes, Outlook is about the only choice for email if you have a smartphone.  But due to Microsoft’s horrible implementation of IMAP, you’ll have to deal with its design flaws.  One persistent problem that is widely reported but has never been fixed is that Outlook cannot properly handle changes to your server’s inbox that take place behind the scenes (e.g., when your mobile phone checks for new messages).  Outlook will bring up an alert stating that the connection to the IMAP server has been lost.  An annoying side effect is that this causes Outlook to reset any flags you placed on messages, such as deletion.  This is not a problem with all other IMAP clients, such as Mozilla Thunderbird or Apple Mail.

Unlike POP3 users, IMAP users need to be especially cautious about storing email on the server.  IMAP excels at this capability, but it can cause you to incur extra storage charges because the server, not your computer, is where all your messages are kept unless you know how to get around this.  For long term archival of email, it is recommended that you create a local collection of mailboxes (e.g. in your Personal Folders data file in Outlook) into which you move messages from the server.  While this will cause them to be removed from the server, it will avoid storage fees.  Using IMAP folders on the server is fine otherwise as long as you are aware of the potential cost.  Also keep in mind that if your Internet connection is lost, you can’t get to your IMAP folders on the server.  So important messages probably should be manually moved or copied to local personal folder storage on your computer.

IMAP Typical Use Scenario
You’ve read some messages in your IMAP inbox and now you delete them.  Unlike POP3 where they will just disappear into the Deleted Items folder, they are simply flagged for removal (Outlook shows them in a struck-out style).

To remove your flagged-for-removal messages, you need to purge them.  In Outlook, for example, use the Purge items under the Edit menu.  In newer versions of Outlook, you can configure it so that switching IMAP folders will automatically purge flagged messages.  You can also configure your email software to purge them when you quit the program.

If you want to move a message out of your IMAP inbox and into a mail folder for longer term storage, you need to decide if you want to store it on the server or locally.  Create folders on the server or in your Personal Folders local storage on your PC and then drag the message from the inbox into the appropriate folder.  This may flag it for deletion in the inbox, so as described above, you’ll want to purge your inbox of flagged messages.

You used to be able create shortcuts on the desktop that would directly open a remote folder via FTP with no intervention. With an open FTP folder window, remote file management was a breeze because it acted like a folder on your hard drive.  This article shows you how to recover this helpful feature.

Drag-and-drop FTP windows are possible using the extended FTP URL syntax that includes a username, optional password, and the server’s address.  Example:

ftp://user:pass@ftpsite.com/directory

Unfortunately, giving an extended FTP URL to IE7 only displays a listing of the folder in “read-only” mode.  You then have to click the Page menu and choose Open FTP Site in Windows Explorer.  That fails because IE7 doesn’t pass forward any user/password credentials in the URL. So then you have to completely retype the URL again. What a drag just to get the old drag and drop mode.

But I found a workaround to preserve the simple shortcut-like behavior we used to enjoy. It works because we completely avoid the browser.

Instead of using Internet Explorer, you use Windows Explorer (the file navigation part of the Windows operating system). To do this, create a batch file and name it something like ftpsite.bat with two lines:

@echo off
start explorer ftp://user:pass@ftpsite.com/directory

(Of course, replace the components of the FTP URL as appropriate.)

Run the batch file by double-clicking it.  At first, nothing will seem to be happening.  After 5-10 seconds it should eventually open up the FTP site in a window like you used to see in IE6. For the security conscious, if you leave out the :pass part (the password) it will prompt you to enter a password.

You can still open extended FTP URLs without having to create a batch file by going to Start -> Run and typing or pasting the FTP URL in the Open box and clicking OK. Basically, as long as you avoid IE7 and use Windows Explorer itself, the extended FTP URLs are honored.

This workaround is compatible with IE6, Windows XP, and Windows Vista.  Since it doesn’t involve the web browser, it also works for users who have non-IE browsers installed as their default.