Just keep one separate C: partition for Vista and all your programs and set the 2nd D: as a data partition. Sure helps if/when you re-install Vista-etc or better still, restoring from a backup image of your C: partition.
Some people do go a bit crazy in my opinion and have many separate data partitions.
I note that some laptop manufacturers are now offering a standard option to have 2 partitions on one hard drive on the 1st boot up of a new machine. That, I truly applaud.
As to the specific size of the C: partition, it is most space efficient if you keep it below 32Gb. But frankly speaking, as you also have a second hard drive and the main is 500Gb, I won't stress-out on that efficiency either and go for circa 96Gb or less.
People who partition are true Luddites. Use an external drive or a 16Gb flash drive to back up your documents and if you spend £12 you can have Acronis which will do it for you. This will save your life one day. All info on one HD = dumb
I'm a Luddite with a 20Gb partition for XP and programmes, all the rest for data and TI to back up to the 2nd HDD. If, as with the latest Net Framework 3.5 update, the XP installation is messed up I can restore it in 3 minutes. I suspect that if I were to have to restore the complete OS and all the data it might just take a little bit longer both to backup and restore.