Have used 40GB, 80GB, 120GB and 160GB combinations on my machines here. What I can tell you is this, for me, 40GB for installation of OS causes lags compared to 80GB. Remember although you may install programs and the like to the 2nd drive/partition, etc... you need sufficient page file space, virtual space and free space.
On desktops the best results I have had are with 80GB drives, single Partition for OS only, a 2nd SATA drive(160GB) split into 2(40GB/120GB) where the 40GB partition becomes the Application Partition.
On laptops the game becomes different, 64bit wants more space always, be it laptop or desktop. I prep a 120GB hard drive for the OS and a 2nd Hard drive from 320 up instead of a OPtical(DVD/CD) drive, with the optical drive being done via USB.
On 64bit Computing, it's not really the Hard drive size that makes the difference, although 64bit does perform better with bigger drive sizes, RAM is critical on 64 bit computing, personally I would use no less than 8GB Ram with 64bit, I have tried with 4GB and find no significant performance difference on my systems other than more stability.
Hope the Essay helps, sorry for the long post.