Seen this question crop up quite a few times on various forums, will do my best to answer (bearing in mind I own a GW-M5600 only

)
The main advantages of the GW-5000 are
* DLC coating to case
* Screwback
* Multiband6 (if you live in or visit China!)
* Supposedly better resin used on band and bezel
* Made in Japan
Of course in real life the main difference between the GW-5000 and GW-M5600 is price, the
GW-5000 can be had for around US$400 from Japan where as the
GW-M5600 can be had for more like USD$90 wherever you live in the world.
Back to the original question. For me it isn't worth the extra, but this is given I alrady have a GW-M5600 and three DW-5x00 series screwbacks. If I was buying without any of these I'd be tempted, it certainly carries the kudos of being one of the top end G-Shocks.
Let us know what you decide
