#1 Get and use a 'file brush' – clean the file after use EVERY time.
#2 Dedicate a draw for them or better still make a rack up as suggested above.
#3 We all have tools lying around whilst 'on a job' but always get into the habit of clearing up for 5 or 10 minutes at the end of your allotted time in the workshop. Do a deep clean every so often – its amazing what you find!
EXCEPT where drills are concerned. Always when finished drilling, clean the drill with a wipe and put it back into its box. If the shank is damaged or the drill needs sharpening put it in upside down! This will remind you next time to dress or sharpen that drill. That way the drills will always be there!
Admission – My big weakness is Allen keys – I must have about 6 sets each of metric and imperial all jumbled up!