This D drive: is it a separate physical drive, or a second partition on your single HDD? If the latter, odds are that since Ubuntu works just fine, there’s nothing wrong with your HDD.
If you boot off your Vista DVD, you should be able to do a System Restore. Before that, as Vista tries to start, press F8 right at the start and you’ll get a menu. Select ‘Last Known Good’.
“Recovery Media” generally only formats your hard drive and reinstall the OS. Since in the OP you seem to care about your files, I’d do as Alex_Dubinsky suggests and use your linux partition to back your files up now.
It’s certainly possible that a CRC error is just a temporary glitch that chkdisk can fix, but if it’s a HD problem, any messing around you do lessens the chances of getting working data off.
Once that’s done, you can do as Quartz says. If that doesn’t work, a Repair Install might.
I know this sounds like magical thinking, but do what I wish I had done before I went to all the trouble of restoring my hard drive from backup a few weeks ago: double-check your connections. I know it’s a pain in a laptop, but just open it up and disconnect the hard drive and re-connect it, then try again. It really might be worth it.
If the drive is dead and you cant get your files off, you can try something like spinrite. You’ll need to pull the drive and install it on a computer running windows first.
At this stage, I wouldn’t bother backing up anything but your data. If you put your data where Windows wants you too (My Documents), that should be C:\Documents and Settings\username.
Err, you shouldnt be overwriting those folders or files on your new install, especially if you were having problems earlier. Just get your media files and documents. If you use IE get your favorites and if you use firefox get its profile.