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Sue gets an average of forty-five emails each morning, as does Bob.   During the course of the day, both will receive thirty or more emails. 
Sue skims through the morning’s emails, looks for the interesting ones, and says she’ll get to the others later.
Bob works his way systematically down the list, just as if he was opening snail mail, and deals with each one.
At the end of the day, Sue will have dealt with most of her mail – albeit in a somewhat haphazard fashion.   Sometimes she misses an important email, sometimes she loses track of one, because it’s no longer visible on the screen.
Because she chooses which ones to attend to, she looks for the ones that are easiest to deal with first.  Difficult ones get left until later, and often don’t get the attention they deserve.   Her Inbox becomes full of clutter – and she seldom knows where important emails are.
Bob, who wouldn’t necessarily call himself the most disciplined person in the world, still aims to use a four choice system that he brought over from his days of working with paper.

1. act on it
2. pass it on
3. file it
4. discard it

Act on it.   Obviously not every email can be acted on there and then.   Some may need the involvement of co-workers, or considerable activity to bring it to fruition.   Whatever the case, unless Bob can deal quickly with an email, he prints it out, and puts the hard copy in a marked folder on his desk.   If it’s urgent, it goes in the Today folder, if it requires further input, it’s put in a separate folder, and so on. 
The original email is also placed in an appropriate email folder, creating one if necessary.

Pass it on.   If the email needs to be passed onto someone else, Bob either forwards it electronically, with a note saying he’s seen it, or prints it out and ensures that the worker gets the copy straight away.

File it.  If the email is information that is needed for future reference, he parks it in an appropriate drawer on his computer.   If it’s information that only needs a quick perusal and can be discarded, he trashes it.  If it’s information that will require further consideration and thought, he prints it out and makes sure it’s filed immediately in the appropriate file.  One of his aims each day is to read through such information.   For this he sets aside a quarter to half an hour at around about the same time each day.

Discard it.   Bob discards all items that are of an ephemeral nature, or unimportant, such as advertising unrelated to his business, humour (after getting the joke) and so on.   Spam is automatically filtered out, but Bob checks new spam at least once a day, in case something has gotten in there by mistake.

Bob always replies to emails from section one and two, even if it’s just to confirm that he’s received the information, or to let the person know he’s working on it.   Apart from the courtesy aspect, this means the sender knows his email hasn’t gone missing in cyberspace, and that it’s receiving attention.

Sue, however, only replies when she has to give an answer, which often leaves her email senders in the dark as to what she’s doing, or whether she’s received the information.   Certainly in the past, with snail mail, recipients didn’t always confirm that the mail had been received.   However, with the ease of reply in the email system, it’s bad business practice not to reply. 

Bob always checks the email drawers once a week to see what can be trashed.   Because he only keeps what’s essential, this isn’t a long job.   Sue tends to keep all emails on her computer, some in drawers and some not, ‘just in case.’   Consequently when she’s looking for some information, her Find facility will turn up all manner of irrelevant emails, wasting further time.   Back ups of her computer often take far longer than necessary because of all the out-of-date material sitting on her system.

Bob knows his approach may seem pedantic to Sue, but he also knows he loses track of very little in the course of a day.  Sue knows she has some trouble finding emails quickly, but blames it on the system rather than on her lack of discipline. 

Being disciplined with emails seems hard.   Because they don’t pile up on your desk like paper, because they vanish up the screen, often quite quickly, there’s a tendency to think that they’ve been dealt with.    Worse, they’re easily forgotten.

It’s essential to form a plan of attack with emails because of their very emphemerality.

Some suggestions:
Don’t check for more emails until the ones that arrived earlier have been dealt with according to your particular ‘system.’
Don’t say you’re trying to save paper by not printing out important information. 
Emails that are easy to handle, and interesting, shouldn’t take priority over ones that are actually more productive for your business.
If, on the way home from work, or in the middle of the night, you suddenly remember you didn’t deal with an email during the day, then your system isn’t working.    This seldom happens to Bob, but it happens to Sue far too often.