The term goodwill value is accounting term. It is also used more loosely to refer to that part of a company valuation created by the positive perception of the company from clients, customers, and the general public.
This reminds of a test that was performed by AOL to compare the quality of their search engine to the one of other companies, like Google. They gathered people in a room, and asked them to rate how well the results given by different search engine matched what they were looking for. The verdict of the people was clear: Google was better. There was only one issue: AOL Search was always returning the exact same results as Google, because AOL Search was using the Google search engine. So why did people like better the result from the "real" Google? Most likely, because they trusted Google more. That trust has a real monetary value.
Good mergers create value; they create a whole which is greater than the sum of the parts. But I fear that if Yahoo gets acquired by Microsoft, a lot of goodwill value that has built by Yahoo over the years will lost. This would be bad for the people at Yahoo who worked all those years to build this value, and for the web as a whole.
Or as Russ puts it, more succinctly:
Anyone who stays after a MS purchase won't be working there for the love of the company, that's for sure.