As a means of data backup I can think of very few cases in which it ever would have helped, and none of those are common. The common things being dead drive (dead drive is a dead drive and all that), accidental deletion (though I suppose I could kick it to the other partition rather than getting a USB drive/network share/whatever) and something more nefarious (it is a powered drive presumably accessible by the same system).
I like it sometimes if you are in a situation where certain filesystem types are at play and one might not work so well with another. Time was it did allow for dual booting but with Window's current fondness for respecting permissions it is not as nice as it was back in the XP days.
I like it because it means should you actually want to stick the user data on another separate drive later then it is far far far easier for Windows and still somewhat easier for Linux.
In the case of windows I have a few systems out there with multiple "installs" of XP on there and boot.ini in play
http://best-windows.vlaurie.com/boot-ini.html . They are mostly application specific programs that fight with each other and I have not migrated to virtual machines. Said application specific programs earn the client a fortune though so there is that. In one case the Ford car diagnostics tool (called IDS but apparently they have a new one out now) and the Jaguar-Land Rover tool (also called IDS and operates from the same very expensive little box).
I guess you can try booting another OS but I have any amount of USB and DVDs to boot another OS from.
On the flip side the only real downside other than some very old and very crappy programs (again in my case car programs being the usual one to cause me grief here) is running out of space on one or the other and still having a bunch free on the other. For the data drive it is not much different to running out of space in general and I fire up the USB/NAS/whatever. For the program install drive I have thus far been OK really, unless I fill it up with stuff from the data drive when I am too bone idle to put it on USB or something.