Memory test and chkdsk are going to be your best bet. If it still doesn't boot, more than likely you have some system files that have been corrupted. Most malware rely on the OS to be booted and running for it to actuall stop you from doing any type of repairs, but it could have corrupted other things before hand.
You could also sfc/scannow at a command prompt to have it check the system files, but that's a long shot since it goes off a stored copy that could also have been modified.
Last thing I'd do, and I'm not sure if this actually works in Win 7 but does in XP and Vista, would be to delete some of the registry files, the older versions of Windows would recreate them on boot with something of a clean slate, but that's only if you don't have any other options. I would run a recovery rather than doing that unless I didn't have my discs.
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