0.9 / 90 nm process indicates what process it was made on, they smaller, usually the better as they shrink the die they can most of the time (up till now with the Pentium 4) push the clock speed further.
The difference between the 0.13 micron and the 0.9 Micron 3500+ is that the 90 nm 3500+ runs cooler, overclocks better ( more head room) and runs at 2.2 Ghz. The .13 micron 3500+ runs at 2.4 Ghz (newcastle), runs a little hotter and does not overclock aswell.
Sorry If I messed up with the Newcastle frequency, AMD change their number scheme so much I have a hard time remembering it all.