Dave Mason defends the honor of linked servers:
I seem to be in the minority when it comes to SQL Server linked servers. When it’s another SQL Server instance on the other end, I quite like them for administrative purposes. But other SQL pros have some reservations and gripes. I’ve even seen the word “hate” thrown around freely. Most of the complaints seem to fall into one of these categories: poor performance, insufficient permissions, poorly configured security, and challenges related to remote execution of queries.
I think Dave’s reasoning makes a lot of sense. Linked servers are not themselves evil. I think it’s likely a mistake to incorporate them into your mainline application (a mistake I’ve made in the past), but for the kinds of administrative tasks Dave mentions, it’s certainly not a bad idea.