I deleted the old Java versions and installed the latest version. Downloaded and ran the ATF Cleaner. Downloaded and ran the Malwarebytes' Anti-Malware and performed the quick scan. It found 1 infected file, which it disinfected, and I restarted the computer afterwards per its instruction. Here is the MBAM log:

Malwarebytes' Anti-Malware 1.46
www.malwarebytes.org

Database version: 4994

Windows 5.1.2600 Service Pack 3
Internet Explorer 8.0.6001.18702

10/29/2010 8:01:40 PM
mbam-log-2010-10-29 (20-01-40).txt

Scan type: Quick scan
Objects scanned: 152348
Time elapsed: 7 minute(s), 40 second(s)

Memory Processes Infected: 0
Memory Modules Infected: 0
Registry Keys Infected: 0
Registry Values Infected: 0
Registry Data Items Infected: 0
Folders Infected: 0
Files Infected: 1

Memory Processes Infected:
(No malicious items detected)

Memory Modules Infected:
(No malicious items detected)

Registry Keys Infected:
(No malicious items detected)

Registry Values Infected:
(No malicious items detected)

Registry Data Items Infected:
(No malicious items detected)

Folders Infected:
(No malicious items detected)

Files Infected:
C:\WINDOWS\system32\cpnprt2.cid (Trojan.Agent) -> Quarantined and deleted successfully.