Depends on you r situation really... If you were to respond go along the lines of thanking them for there letter state you were not aware of any other registrations of the name (nominet may hold sway with the .org.uk but not sure anyone else would?) If they did not state you about trade mark you can either not mention it at all or state when you registered the name you had checked to see if there were any trademarks and there were none decided it was a good name. Possibly mention you have invested time and monies in it are not sure what to do but will probably seek some advice and see how they play from there…?
My thoughts on replies are either be civil yet firm or don’t bother at all…? If you ask for money outright or are rude they will often use your replies in any evidence witch can paint you in a bad light so to speak... Also remember the way and manner that you reply can also be an indication to them of how long to prepare and how good a lawyer etc to allocate to your case this can have some distinct advantages for you if played well
this might also help
http://www.chillingeffects.org/trademark/faq.cgi