Here's the MBAM log. I'm not sure why it says it didn't do anything - there must have been two logs, because the one I meant to save definitely had the deleted/restored/etc. messages.
Also, I just turned on "view hidden files" and all my desktop icons are there (they were just hidden), but the start menu and quick launch icons are still missing. I found a "System Check" icon on the desktop, followed it to its location, and deleted it and associated files.
And, of course, I'm still worried I might have a rootkit.
Malwarebytes Anti-Malware (Trial) 1.60.1.1000
www.malwarebytes.org
Database version: v2012.03.22.04
Windows Vista Service Pack 2 x86 NTFS (Safe Mode/Networking)
Internet Explorer 9.0.8112.16421
Dan :: DAN-PC [administrator]
Protection: Disabled
3/22/2012 6:01:37 PM
mbam-log-2012-03-22 (18-07-03).txt
Scan type: Quick scan
Scan options enabled: Memory | Startup | Registry | File System | Heuristics/Extra | Heuristics/Shuriken | PUP | PUM
Scan options disabled: P2P
Objects scanned: 215972
Time elapsed: 5 minute(s), 5 second(s)
Memory Processes Detected: 0
(No malicious items detected)
Memory Modules Detected: 0
(No malicious items detected)
Registry Keys Detected: 0
(No malicious items detected)
Registry Values Detected: 1
HKLM\SOFTWARE\Microsoft\Windows\CurrentVersion\Run|BGNKveQAbc.exe (Rogue.FakeHDD) -> Data: C:\ProgramData\BGNKveQAbc.exe -> No action taken.
Registry Data Items Detected: 3
HKCU\SOFTWARE\Microsoft\Windows\CurrentVersion\Explorer\Advanced|Start_ShowMyComputer (PUM.Hijack.StartMenu) -> Bad: (0) Good: (1) -> No action taken.
HKCU\SOFTWARE\Microsoft\Windows\CurrentVersion\Explorer\Advanced|Start_ShowSearch (PUM.Hijack.StartMenu) -> Bad: (0) Good: (1) -> No action taken.
HKLM\SOFTWARE\Microsoft\Windows\CurrentVersion\Policies\System|DisableTaskMgr (PUM.Hijack.TaskManager) -> Bad: (1) Good: (0) -> No action taken.
Folders Detected: 0
(No malicious items detected)
Files Detected: 1
C:\ProgramData\BGNKveQAbc.exe (Rogue.FakeHDD) -> No action taken.
(end)