Helping people with computers... one answer at a time.
When replacing a motherboard you can almost certainly use your hard disks, the question is how much additional work and configuration you might need.
If I get a new motherboard for my computer, can I use the hard drives that I have with it? From what I've read, I expect the current C drive operating system won't work with a new motherboard, but if I installed the operating system on my current D drive, and used that as the new C drive, would it work, or would I be risking the information on the drive? (I really don't want to lose all my pictures!) I would then want to put my current C drive in as my new D drive, and delete the old OS off that. Also would the programs get confused as to what drive they are on?
The short answer is yes you can probably do what you're suggesting. In fact, it's one way I'd probably approach the problem myself.
But we also need to set some expectations about what it is you'll have when you're done.
First, if you get the exact same motherboard as a replacement you can probably just avoid the issue complete. Chance are you can just plug C: into C:, D: into D: and things will likely just work.
If you have a different motherboard (replacement is always a good time for an upgrade :-), or you just want to play it safe, then plugging your new drive in as C: and your old C: drive in as D: makes a lot of sense, and will in all probability work just fine.
You'll install Windows onto your new drive, and once done everything that was on your old C: drive will appear on your new D:. Very handy, and you should be able to copy those pictures off with no problem.
But you raise a good issue: everything may not be what you expect.
Yes, your programs will be very confused. For one thing, since you've installed Windows from scratch onto your new drive, the programs will no longer be "installed". They'll be present on the D: drive, but they'll no longer appear in the Start menu. If you do manage to locate and run one of the programs, it's likely that it'll fail since all of its settings that were kept in the Windows registry are no longer in the registry of the newly installed Windows. Temporary locations or other support files that are part of setting up a program are, effectively, wiped out with a clean install of Windows.
The files will still be on the D: drive, but Windows, and the application, will have lost track of them.
Now, there are applications out there that you can purchase that claim to be able to "move" installed programs from one computer to another, or from one hard disk to another. Because of the complexity involved in doing so reliably, I'm somewhat skeptical - but it's skepticism born of ignorance, as I've not tried such a utility. Yet. I do have a copy of one of the more reputable programs on my shelf for evaluation later this year.
Without such a utility, the solution is to reinstall all of your applications from their initial install CDs. In my opinion that's one of the most reliable approaches you can take. It is a bit of work - but once done, you have not only a fresh, clean install of Windows, but the same for all of the applications you chose to reinstall.
Once the applications have been reinstalled, you can copy over data files from your old drive and be on your way.
We're not done! I can't let this go without this comment: You're not backing up, and you should be.
If you have important things on your hard drive that you don't want to lose and they're only on that hard drive - you're taking a huge risk. Some day that hard disk might die - without warning, and without recovery. You could easily lose everything that's on it. I strongly recommend you take this opportunity to invest in a backup strategy that will cover your assets in case of a disaster scenario.