Hm, I missed the news about Apple filing a US trademark for WebKit earlier this May. I think it’s not a big deal.
A lot of free software project names are trademarked by the authors in some part of the world. Most are used defensively so that others cannot file the same trademark, but some are used for preserving brand identity (see Iceweasel).
In the worst case, projects have changed names over trademark or even non-trademark name clashes. Phoenix→Firebird→Firefox, Gaim→Pidgin, and Ethereal→Wireshark are three high-profile examples.
If the WebKit trademark is granted, depending on how Apple decides to guard it, others in the US will probably go back to the KHTML name. Considering there are other big stakeholders in the WebKit world now (Google being the biggest one), I don’t think Apple will risk fragmentation, but who knows.
In my opinion, among “intellectual properties”, trademark is likely the least of our concern. I could be wrong though; I haven’t seen much discussion around it.