How do you keep track of all the web apps you use to run your business?

I use Roboform which stores all my username/pwd credentials at one place. They also have a cloud version which you can use to access your data from most of the devices.

To share them with your employees, maybe you can first delete your passwords from the local roboform datatbase, export the file and use it as a template for all your employees.

Bookmarks, lists etc are one option.

Personally I would hope to make use of their API's to combine them all into one company intranet. Or look for an all-in-one solution.

Why not have an "important links" page on your intranet, sharepoint, internal wiki, etc?

I can't think of any better way to make sure everyone has access to all the links you say you need to run the business.

Of course, you also want to make sure only the proper employees are accessing services they're supposed to (ie marketing shouldn't be on your recruiting service) - but that should be manageable via ACLs or similar.