First of all you mention you have tons of RAM. Resources and RAM have nothing to do with one another. You could throw all the RAM you wanted at Win9x and resources would be the same as if you run with 32MB. Resources are unlimited with W2K.
With that being said, a properly configured computer loaded with W2K does not need to be rebooted to free resources. The W2K kernal is light years better than the 9x kernal when it comes to freeing resources and memory management. Due to caching, especially with larger amounts of RAM, you are better off not rebooting since the information you may need has a good chance of being stored in RAM. This means it doesn't have to find it on the disk. If you reboot, you force all information to be read from disk until W2K starts to fill the cache up with frequently used information again.
If you have problems with W2K slowing down between reboots, you either have a misconfigured system or some really shoddy software.