I think there are three different, but related, aspects of this whole brouhaha on Boardgame Geek that everybody can take away as lessons learned if they choose -- although some may not.
The first is Games Workshop's aggressive defense of its intellectual property. I was unaware of the Warhammer/World of Warcraft connection and I can understand how GW may feel quite burned by that experience. I think they were within their legal rights on 90% of what they claim, although on some specific points their IP policies make claims unsupported by the actual state of the law. The reality is that those assertions will probably stand until they tangle with someone with the economic resource sand interests to contest it. On the other hand, there's serious grounds for doubting the wisdom of their approach. Making a significant portion of your most dedicated fans angry with you seems like a very bad business idea. While most of GW's customers are not on BGG or members of GW fan sites, those who are tend to be the opinion leaders in their groups and probably have an influence outside of mere numbers,
The second lesson is BGG's response to GW's demands. Here I think there are some legitimate ground for criticizing some details of how BGG responded, but BGG's overall response was a prudent one given the magnitude of the legal threat and the relative peripheral nature of the possible benefit. Games Workshop is just one company whose products are on the site and it doesn't make sense to risk all the other valuable content here related to more consumer-friendly companies for the sake of the products of a company that doesn't appreciate the free advertising. BGG is a growing site and becoming the premiere game-related site in the world devoted to all games. GW benefits more from BGG than BGG needs GW. It's unfortunate that the controversy broke out while Aldie was unavailable to address it quickly, but it appears to me that BGG is taking lessons learned from the experience and implementing policies and procedures that will reduce future problems.
The third lesson is for us, the users of BGG. One thing many of us could do a better job of is respecting the legitimate intellectual property rights of game publishers. I see an awful lot of stuff posted on BGG that really is egregious copyright and trademark infringement. We have open advocacy by some of making your own copies of games so you don't have to buy it We have users scanning high-resolution images of the complete components of some games. In many cases users are posting clearly derivative works without bothering to ask permission (which many companies would probably grant -- see the nice alternative map available as a download for Bonaparte at Marengo. For example, I often like to post examples of components when I am writing a game review. I am always careful never to scan in complete copies of the component in question -- a part of a map, a few examples of the counters, an extract of a play aid, one or two cards. This is fair use. Scanning in all 108 cards at full-size for a card game is not. Lastly, fans of a game should realize that the content they generate (let's say a really nice, upgraded player aid with snazzy logos and photos of miniatures) may not be theirs, even if they did a lot of work on it. Spend your effort on companies that appreciate and encourage that kind of work. Don't waste your time supporting a company that doesn't.