Erm, where do I start... I have a CD3000 myself at home and in the studio I work we bought 2 S5000s about 4 months ago.
The major difference is in the OS. The S5000 has a much better interface than the S3000. Also, the soundquality is crispier than the S3000. + and it a big + the S5000 can read .wav files. bye bye Akai format. The 5000 can still read your old CD-ROMs, but imagine you can link your S5000 to your computer. You manipulate samples on a big 17" screen and just download them to your S5000 and vice versa.
yes, the S5 and S6000 now have this think called LINKSys, a program you have on your computer, where you can control EVERYTHING very very easily, thru..... USB !!! (with the new USB extension).
I sold my S6000, it had 256MB of RAM, it was quite good, BUT I had to buy a SCSI hard drive and all this expensive stuff.. also the filters were almost impossible to control before... Now it is MUCH better.. no need of any SCSI peripheral, you can pop in AKAI CDROMs right on your PC and load them in the sampler, drag and drop instruments in the machine right on your screen... I mustt say they did a GREAT additions
so yes, definitly different between a 3000 and the latests.