Re a need for second hdd in notebooks for data, here's how my laptop is set up.
I have a main working OS partition, that is used for testing new software as well. It eventually becomes dirty and is replaced.
A second backup OS partition which is used to replace the main OS partition when it gets dirty. This partition is updated when new progs are added, tested, and proven stable.
A third OS partition in case the second becomes unstable.
A lot of people might think this is overkill, but i hate reformatting and starting from scratch. Program tweaks, personalizations, patches, and OS updates can chew up weekends and Gigabytes of download.
As I said earlier, I haven't reinstalled in 2 years.
I use a partition manager called Bootit for all this. It allows me to boot into either of the three OSs and is a good partition copier and imager. The data is common to all as it is on a separate partition, even email, favs, IE history etc.
Every so often I copy the OS partition onto an external notebook drive via USB2 port and hdd case.
Data is kept on its own partition. Critical files are scheduled for backup to internet once a day, and onto local hdd backup partition twice a day.
Once a month I copy the data partition onto external drive and archive onto cd probably every 2-3 months.
Re keeping a partition clean, i use kerio or ZAP, adaware, NAV, and a reg cleaner like JV16 powertools.