Installing Combo Update If I Already Have OS X 10.8.2

You could try it. It may fix something if the something was modified in the update.

However, the something may be incompatible third-party software.

It could be as you suspect, something just didn't go right in the install. The combo may fix it, or you may have to reinstall completely.

If you've ever installed anything that purports to help your Mac, that's likely the culprit.

How many items do you have in your System Preferences > Users & Groups > Login Items?

Well, that was worth a shot. Other than that, do you have any AV software installed? Or any other "cleaning" type of apps?

If you uninstall Sophos, does the performance improve? The other two (Rip, Smart Converter) seem to be rippers? I don't know if they can cause a problem or not. I'd try uninstalling Sophos - are you running Windows? If not, why do you feel you need Sophos? Since there are no viruses currently for Mac, the guard seems to be a bit superfluous.

I'd try the Sophos; after that, I'd try the rippers - we aren't really allowed to discuss anything that has to do with circumventing DRM/copyright issues, so depending on what you use those for, we might not be able to help troubleshooting those. Couldn't you scan your flash drives on the office Windows machine before you take them home?

Uninstall Sophos

1) Did you uninstall using Sophos' uninstaller? Just wondering if there is something still arround.

2) What is slow about the bootup? Is it stuck on the gray screen for a while, or is it slow loading up all the programs that were left open when you restarted?

3) You might try ClamXAV for scanning those files you transfer. It can just sit there and not do anything until you want to scan those files with it. However, you might be able to set up Sophos to not be so intrusive, also.

Thomas has a lot of good advice, here: Mac Malware Guide