Well, after a little googling, I've diagnosed myself as suffering from a fairly severe case of Barotrauma, as I felt intense pain and my balance was effected, previously described as a feeling of general wierdness in my head. Looks like I need to clear my Eustachian tubes. I'm going to try using steam first, and if that doesn't work I'l try carefully pushing the air out. Failing that it's a trip to the doctor for some decongestants.
I really think Barotrauma should be common knowledge. There should be a little info card in the back of the seats on the plane or something. Anyway, here's a link to some info that I found: