I've done a number of different modifications for several different clients. The majority of them are to add new "States" and "Transitions" to support the client's change control, and SOX Compliance in once case. That particular client also wanted to enforce security on WHO could change the states in certain transitions - and who the Work Item could be assigned to.
I've also added a number of fields, common is an indicator of an "Emergency Change", additional priority fields - and fields specific to the clients line-of-business.
If you use the "Template Editor" power tool - it is very easy. But follow normal best practices of any development. Have a development server seperate from your production TFS Server (or at very least - a test Team Project). Put your template(s) under version control (I like a seperate Team Project for "TFS Implementation" And make small changes incrementally.