I also have an issue with freezes since the upgrade to mountain lion. Can not really link this to .EXE files.
The latest log-file entrys after a freeze:
2012-09-24 06:06:13,000 kernel[0]: Sandbox: sandboxd(1073) deny mach-lookup com.apple.coresymbolicationd
2012-09-24 06:06:15,000 kernel[0]: AppleUSBMultitouchDriver::_deviceGetReport - DeviceRequest for reportID 0x0 returned with result 0xe000404f - retrying
2012-09-24 06:06:19,000 kernel[0]: AppleUSBMultitouchDriver::_deviceGetReport - DeviceRequest for reportID 0x0 returned with result 0xe000404f - retrying
2012-09-24 06:06:23,000 kernel[0]: AppleUSBMultitouchDriver::_deviceGetReport - DeviceRequest for reportID 0x0 returned with result 0xe000404f - retrying
2012-09-24 06:06:31,000 kernel[0]: AppleUSBMultitouchDriver::_deviceGetReport - DeviceRequest for reportID 0x0 returned with result 0xe000404f - retrying
2012-09-24 06:06:35,000 kernel[0]: AppleUSBMultitouchDriver::_deviceGetReport - DeviceRequest for reportID 0x0 returned with result 0xe000404f - retrying
2012-09-24 06:06:39,000 kernel[0]: AppleUSBMultitouchDriver::_deviceGetReport - DeviceRequest for reportID 0x0 returned with result 0xe000404f - retrying
2012-09-24 06:06:43,000 kernel[0]: AppleUSBMultitouchDriver::_deviceGetReport - DeviceRequest for reportID 0x0 returned with result 0xe000404f - retrying
2012-09-24 06:06:47,918 WindowServer[85]: handle_will_sleep_auth_and_shield_windows: no lock state data
2012-09-24 06:08:31,000 kernel[0]: AppleUSBMultitouchDriver::_deviceGetReport - DeviceRequest for reportID 0x0 returned with result 0xe000404f - retrying
2012-09-24 06:08:58,931 WindowServer[85]: CGXDisableUpdate: UI updates were forcibly disabled by application "Dock" for over 1.00 seconds. Server has re-enabled them.
2012-09-24 06:08:58,932 WindowServer[85]: reenable_update_for_connection: UI updates were finally reenabled by application "Dock" after 3.41 seconds (server forcibly re-enabled them after 3.41 seconds)
2012-09-24 06:09:06,815 WindowServer[85]: CGXRegisterWindowWithSystemStatusBar: window b already registered
2012-09-24 06:09:14,348 CVMServer[101]: Check-in to the service com.apple.cvmsCompAgent_x86_64 failed. This is likely because you have either unloaded the job or the MachService has the ResetAtClose attribute specified in the launchd.plist. If present, this attribute should be removed.
2012-09-24 06:09:14,461 CVMServer[101]: Check-in to the service com.apple.cvmsCompAgent_x86_64 failed. This is likely because you have either unloaded the job or the MachService has the ResetAtClose attribute specified in the launchd.plist. If present, this attribute should be removed.
2012-09-24 06:09:32,000 kernel[0]: USBF: 5710.739 AppleUSBEHCI[0xffffff802771c000]::Found a transaction which hasn't moved in 5 seconds on bus 0xfa, timing out! (Addr: 3, EP: 0)
2012-09-24 06:09:36,000 kernel[0]: AppleUSBMultitouchDriver::_deviceGetReport - DeviceRequest for reportID 0x0 returned with result 0xe000404f - retrying
2012-09-24 06:09:40,000 kernel[0]: AppleUSBMultitouchDriver::_deviceGetReport - DeviceRequest for reportID 0x0 returned with result 0xe000404f - retrying
2012-09-24 06:09:44,000 kernel[0]: AppleUSBMultitouchDriver::_deviceGetReport - DeviceRequest for reportID 0x0 returned with result 0xe000404f - retrying
2012-09-24 06:09:48,000 kernel[0]: AppleUSBMultitouchDriver::_deviceGetReport - DeviceRequest for reportID 0x0 returned with result 0xe000404f - retrying
2012-09-24 06:09:52,000 kernel[0]: AppleUSBMultitouchDriver::_deviceGetReport - DeviceRequest for reportID 0x0 returned with result 0xe000404f - retrying
2012-09-24 06:09:56,000 kernel[0]: AppleUSBMultitouchDriver::_deviceGetReport - DeviceRequest for reportID 0x0 returned with result 0xe000404f - retrying
2012-09-24 06:10:00,000 kernel[0]: AppleUSBMultitouchDriver::_deviceGetReport - DeviceRequest for reportID 0x0 returned with result 0xe000404f - retrying
2012-09-24 06:10:18,300 mdworker[1099]: Unable to talk to lsboxd
2012-09-24 06:10:18,331 mdworker[1098]: Unable to talk to lsboxd
2012-09-24 06:10:18,000 kernel[0]: Sandbox: sandboxd(1100) deny mach-lookup com.apple.coresymbolicationd
2012-09-24 06:10:19,172 sandboxd[1100]: ([1099]) mdworker(1099) deny mach-lookup com.apple.ls.boxd
2012-09-24 06:10:19,234 sandboxd[1100]: ([1098]) mdworker(1098) deny mach-lookup com.apple.ls.boxd