ShrodingersCat, your post was so funny! 
Let's see... how to tame the paper jungle monster...
It used to be part of my job to set up filing systems or reorganise
a current system to make it more user-friendly. I kinda enjoyed
making order where there was none.
I had a really handy hardcover A4 file with 30+ 'pages' you could
flip like a book and each 'page' was indexed with a no. to
represent dates of the month. Documents that needed tending to on
particular dates were placed in the relevant slots so every
morning, all I had to do was flip my master diary and flip that
file-book and I can get started liao.
I also had a lot of colour coded L-plastic folders. Red is for
'Urgent' or 'Priority', Yellow for 'Pending' etc. I'll scribble on
post-it's and stick them onto the folders too so I'd know at a
glance that the folder is for "Upcoming Directorial Conference" or
"AD&D", etc.
I also had a three-tier tray for "In", "Out" and "Pending" for my
boss or colleagues and the mail distribution chap to use.
If I can't do the filing soon enough, I'd band them up together and
slap a post-it on the stack so when it's time to do the filing, I'd
roughly know where they're supposed to go into.
At the end of everyday, before I left the office, VERY IMPORTANT -
clear your desk of clutter! If you can't, at least make sure you
have organised stacks so you'd know where to continue the next
morning.
Another tip, make sure another colleague or two knows your filing
system so that if you're on leave, they don't have to keep calling
you. Or even if they had to
call you, you're organised enough that you can give clear
instructions over the phone - "It's in the Red Plastic folder on my
top drawer on the right cabinet, keys are with da boss."
Even if your workstation is messy, let it be an 'organised mess'!
Appear in
control of the situation, even if you are drowning in the sea of
paperwork!
Your bosses won't nag at you so much if they think that you are on
top of it all! 
Erm... not quite sure if I've answered your questions cause
sometimes, I tend to go off at a tangent. Well, hope
the tips help! 
