Well, in-use files should no longer be a problem if the backup software uses Window' s Volume Shadow Copy or sometimes called Volume Snapshot Service (VSS) - which most newer ones do. I agree, backup and restore is a complex task, but I don't feel users should know anything about how it works and that includes pop-up windows telling them it was or was not successful. If they get a message everyday, most users will become numb to the repetitive task of clicking ok to a daily backup message and might not even read it half the time or at all. Its better to know something went wrong before the user tells you. Just because they get a message that something bad happened, doesn't mean they will drop everything to tell you about it. I know many will wait until they run into you in the hall, at the pop machine, or when something really bad happens and they can't work.
User: "Hey Jer, can I get you to come look at my computer? Something about an invalid disk error..." [On the walk back to his desk...] User: "I've been meaning to talk with you. My machine has been giving me these pop-up messages lately." Jeremy: "What pop-up messages?" User: "I'm not sure, something about backups. I've just been hitting ok." Jeremy: "How long has this been happening?" User: "I don't know... A couple weeks? Been meaning to tell you, just been busy." [20 mins and one failed hard disk later...] Jeremy: "Looks like your hard drive failed. I'll try some things to recover it, but it doesn't look good. I just check the backup logs... Looks like the last good backup was 3 weeks ago, hope you haven't worked on anything important since then..." User: "...." (stunned silence) Jeremy: "Probably should have told me about those pop-up windows sooner..."
See my point?
I'm all about the adage, "The right tool for the right job". If your going to be burdened with having to manage and administer Windows Workstations, use tools that work the best, fastest, and easiest for the job at hand. This usually means Windows based applications that have a friendly centralized administration interface that can scan the network or preferably integrates into your directory service of choice or at least Active Directory. I would use something that can push install its backup agent across the network to these workstations so you don't have to worry about msi files or pushing files with login scripts. Something that is probably policy based so you can work on groups of workstations and has robust reporting and notification capabilities so you don't have to rely on your users to tell you their backups have been failing.
As far as the simple home users or workstations that aren't part of a large network, buy an external storage drive. Most come with fairly decent backup software, like memeo, that offers real time continuous data protection. External storage is probably the better, relatively cheaper and safer backup medium any way.
Use Linux when its the best tool for the job. Don't sacrifice features, like any of the above I mentioned, just to be an open source purest. In a business environment, use tools that make your life and job easier and then use the time saved to work on your favorite open source project. ;-)
Anyway, just my $0.02....