It is hard to say how a battle over a trademark really alters the position of companies, but Apple seems to be first off the mark in a lot of these situations recently.
Apple has now applied to trademark the Thunderbolt high-speed technology in both the U.S. and Canada. This would seem fine if this was not already assumed to be owned by Intel, who is working on this technology. What Apple does have in their court is a 2010 application for Thuderbolt in Jamaica, which is only going to help things along in both the Canadian Intellectual Property Office and the U.S. Patent & Trademark Office.
Thuderbolt, as the U.S. application states, would then be associated with a whole number of hardware and peripheral items for Apple computers. This would all be around the high speed I/O technology, which is at least the assumption. Right now Intel still clearly lists Thuderbolt as one of its owned trademarks, but this is has not necessarily been verified at the governmental level.
There is not telling exactly what this means for the two companies now, and it actually seems as though Apple helped with some different developments when it was still called Light Peak at Intel. This could be just semantics in terms of how the companies are going to approach new technologies, but a merger is never out of the question.