This is how I understand 5S:
- Organisation (Seiri)
- Neatness (Seiton)
- Cleaning (Seiso)
- Standardisation (Seiketsu)
- Discipline (Shitsuke)
"Put things in order (remove what is not needed and keep what is needed)" 
There must be a reason for a thing to be in your workspace. Keep only the tools that are in current use and discard obsolete tools. If you need a 12mm spanner, then have one. Do not obtain any more spanners until the need presents itself.
If you find that you're constantly searching for pens even though you KNOW that you have 50 of them somewhere, here's a tip: throw out 49 pens, and put 1 pen in your pen-holder. You'd be amazed at how this helps you focus.
Find a spot for your stapler. Put your 6" rule in the right spot. Put your vernier in the right spot. Put your Post-It notes in the right spot. Throw out anything that you never need to see again. If you need a desk-lamp: get one. Obtain a wrist-pad for your mouse.
"Proper Arrangement - (Place things in such a way that they can be easily reached whenever they are needed)"
The correct tool should have a logical location. It's not enough just to have the right tools in a random tool box: they should be up on a shadow-board. Tools that are used more often should be close at hand: there's a reason that surgeons require their tools to be laid out so precisely.
The logical extension to this idea is that you should know where something is and where it isn't. By maintaining a proper spot for everything you will know immediately if it isn't there. You won't waste time searching for a stapler: you'll know immediately that someone has pilfered it and you need to go get a new one.
When you ask someone if they have a pen it's interesting to see if they reach for exactly where the pen is - or do they go scrabbling about in their top drawer? If you ask them for the latest quote or drawing, do they reach immediately for the right folder - or do they start sifting through a foot-high stack of randomness?
Further: What's that person's email Inbox like? Do you find that important emails get lost? What's their approach to maintaining track of projects - do they let minor details turn into huge crises?
A person's neatness affects everything they do. By 'neatness' we mean functionally neat, I don't care if you brush your hair or not. I am not a particularly neat person by nature, which means that I have to consciously work to maintain my neatness. I do care if you can't readily access your tools and do not see this as a problem.
"Clean - (Keep things clean and polished; no trash or dirt in the workplace)"
Randomness is the killer of your creativity. The instant that your well-ordered folder of notes, spreadsheets and drawings becomes random you might as well throw it in the bin. The instant a corner of your office become randomness and Junk you have lost the ability to find anything ever again: something might be missing or it might be hidden in randomness, you have no way of knowing.
Do not maintain possession of items that you no longer need - the only thing an obsolete piece of paper can possibly do is cover up something important.
By making your office clean you make it a nice place to be. You make it a nice place for people to visit. You feel good about the work that you do.
"Purity - (Maintain cleanliness after cleaning - perpetual cleaning)"
The trick, then, is to maintain this order. It may seem like maintaining a bare desk is a sign that I waste time on tidying that I could spend on working - that I don't have enough on my plate.
I say that the opposite is true: my clean desk is a sign that when I need to work I am able to. I have so much to do that I cannot afford to waste my time dealing with the sheer volume of randomness that obscures my path. Instead, the usual state of my office is one of readiness.
It may be tempting to designate a small corner of your office to Junk - but this corner will only ever grow. That Junk will become randomness, and that will eat away at your productivity and reduce your ability to deal with the task at hand - your ability to act now.
Whenever you feel flustered, swamped or hectic; simply put everything back into its place. This process will take less than 30 seconds, and I guarantee that you will:
- feel in control
- have the tools at hand to cope with your current challenge
- find some forgotten but actionable item hidden under something
"Commitment (an attitude towards any undertaking to inspire pride and adherence to standards)"
The reason to be neat is because you want have the self-esteem that comes from aiming for excellence in your profession. Control the things you can control, and accept everything else as an opportunity for growth. When you know that all the little things in your life are under control you will be able to concentrate on the bigger issues - and trust to the outcome.
Maintaining neatness - and knowing how to get back to that state after a firestorm hits you - is a way of respecting the work that you do; and thereby respecting yourself also.
This cannot be achieved by making a decision once and then forgetting about it. The decision must be constantly re-affirmed. Neatness is a relationship (a battle) with the randomness in your life.
When you leave a pen in my office I have to do something with it.
I use my desk for all sort of important things that are vital to my sanity and ability to perform my job. I can't just leave the pen sitting there: I need that deskspace to be clear.
I can't put the pen into my penholder and claim it as my own, because I already have a pen there. This second - probably inferior - pen will only add to the confusion in my life.
I can't throw the pen into my top drawer because I already have a spare pen or two in there.
I can't throw it out because you might come back for it.
When you leave a pen in my office I need to get up out of my chair and return it to you. You might think that I'm an idiot, but it's the only way I can see that lets me keep control of my workspace without being wasteful. Keeping control of my workspace is integral to keeping control of my work.
"Hey, this is your pen."
EDIT: Some scoundrel must have left a pen in my office or something today, because I reached for a pen, looked down and found that I had a Bic that I didnt' recognise.