I don't see why you put OS X on what is way too small a partition. Even MicroMat for their eDrive part of TechTool Pro 4.x requires 7-8GB and that is a very minimal system.
There needs to be room. And it should probably be 50% free. A Mac OS X combo update, package installers, use files that are highly compressed and need to use memory and disk space to uncompress and install and update components. A recent 209MB update could easily require 1GB, plus room to write the new files, etc.
Don't use the Desktop. Use a dedicated folder - on another drive.
Don't force the boot drive to use ACTIVE partitions. If you want or need to archive some static files, fine, but not so the read-write head has to move all over and seek.
VM is tricky. OS X may create addresses and allocate what seems like VM, like I am seeing 10GB, but not use it, not write to disk (I don't see any pageouts, hence, no swap files and VM isn't even used, and if it was it would only be 64MB and rarely would it get to 1GB.
/private/var/vm/
Applications could be 2GB and up.
Library can be 1.5GB and up to 10-20GB
System 1-3GB?
There are also hidden directories that take up a couple GB. Download and scan your drives with OmniDiskSweeper and WhatSize.
Use symbolic links, aliases, and NetInfo Manager to put folders or even "Users" or a specific user home directory, on a 2nd disk
drive.
/Volumes/
volname/Users/my_homedirectory
Don't try and make Mac OS X into linux or behave as if it had the same structure, slices, or needs - - it doesn't.
You want a fast system boot drive, buy a 10K Raptor or 500GB model from WD, Hitachi or Maxtor. (I've seen 73-75MB sec from the outer tracks). And yes, partitioning 500GB (475GB formatted?) might make sense - done right.
Mac Pro 2GHz 4GB 10K Raptor 23" Cinema Mac OS X (10.4.8) WD RE16 RAID DW 4.0 APC RS1500 Vista RC1