Why does Android offer updates for all the gmail accounts on the phone? I have multiple gmail accounts on my phone and I get Market and other updates listed for each of these accounts. That is simply annoying.

How can I disable that and instead set one account as my primary account for updates and such like?
You probably used different Google accounts for different apps. Switching accounts will show different apps.

I guess all you can do is uninstall the apps from one account, change accounts to the one you would like to use and then reinstall them.