When Salesforce.com acquired Heroku I was horrified that things were going to go downhill. Heroku has continued to get better and better as far as i'm concerned! Hopefully the trend of acquihires and product shutdown stops though.
There are definitely exceptions to the rule. Unfortunately, I'm pretty sure eBay isn't one of them.
I felt the same way when they picked up Desk (formerly Assistly). I have been pleased that they continue to push the product forward since the acquisition.
Salesforce has mostly bought things and kept it going