Mine is quite simple. It's modeled after the Julian Calendar (JC). Everyone in the military knows it.
The JC is a 10 year calendar. For 6000 - the 6 equals the last digit for the year - 1966, 1976, 1986, 1996, 2006, etc. The 000 refers to the day of the year. For example, 1 Jan 06 was 6001. Today is 14 Jan 2006. In the JC the date is 6014.
Right now I have batches 6001 and 6002 in primaries and 6003 is scheduled for tomorrow. I could use the JC dates for my brews but that would not tell me how many batches I made that year.

I just use the number for the batch.
I know I will NEVER brew 1000 batches in a year and could actually delete a zero or two, but since I use the JC at work it is just simpler for me to continue using the 4 digits at home.
I have seperate folders (in Word.doc) for the year, 1999, 2000, 2001, etc. to keep the numbers apart. It's not really a problem because I name the files like this:
6001-Chili-Pepper
6002-Traditional-Mead
6003-Czech Budvar-Billvar