Yes, you can use "bad DIMMs", both in Linux and in Win9x. Look up the "badram" driver for Linux, I think it needs to be compiled into the kernel, but it can be used to map out ranges of physical memory to avoid being used.
Similarly, with a little EMM386/HIMEM/RAMDISK/SMARTDRV magic, you can map out a bad chunk of RAM under DOS, and Win9x as it boots will respect and import the memory-usage tables set up by those drivers under DOS mode.
There is no such solution that I am aware of for NT-based OSes like W2K/XP, although there is a way to limit the total maximum physical memory that the OSes will use, that might work if the bad range of memory addresses are near the end.