Hi Stephen,
I agree with Kristen - CRM Fusion is particularly helpful for data cleanup. I use their Power Grid tool frequently and I think this tool could help you a lot. They also help merge duplicate records in bulk.
There are many tools to help with the pain point your describe. Check out
Reachforce and NetProspex (they'll have a feature coming out in a month or two that will create consistency among company names). There's also a free app in the SFDC Marketplace called "Mass Update Wizard" that you should get.
You can also set up triggers based on the company name field and/or email address field. For example: if email address contains @nike.com or company name starts with Nike or equals Nike or Nike Inc -> edit company name to be Nike, Inc.