as far as it is announced, it will be a true 32-bit system. This means, if you still have some W3.x software or DOS software, they will not work anymore.
Software made for W95 or W98 will work.
It is pretty much the same as with NT, no DOS or W3.x software, most of the W95 and all of the W98 software works.
NT uses internal handles for port access, i.e. printer and serial ports. This is different to DOS. Win 3.x and W95/W98 are still leaving the Windows platform to access these ports, also you are shown a nice graphic that the printer is spooling etc, but if you check the status bar, you see the DOS symbol there while printing.
This is only one of the changes....but for many people it is a very expensive one, you will need to upgrade your existing packages to 32-bit editions (if the manufacturer re-wrote the software at all...).
W98 is capable of dealing with 32-bit software if it is not specially written for NT (the handler problem) but it is the end of a production line soon...