We are probably strange, but we tip the server as if they were a server in a regular (non cruise ship and non upcharge) restaurant. For example when having brunch at Palo, we would compare it to what brunch would cost at someplace like maybe Narcoosee's (as that is the only restaurant in common to Disney fans that I can think of that serves brunch). Even though we are only paying $30pp we get $60-70 (if not more) of value from our meal and tip on the value rather than the cost.
At Palo Dinner we compare it to what we would spend at a restaurant such as Napa Rose, and tip on closer to about $100pp, and if we ordered a lot of alcoholic beverages, we would factor the number of drinks, and not so much the cost. It isn't more difficult to bring a $45 glass than a $16 glass of wine. Both these experiences are based on our trips on the Wonder where we have had Hristo as our excellent server and he always took extra special care of us.
At Remy, we compared the tip as if we were dining at Victoria and Albert's, also we added on some Kobe Beef, both wine pairings and anything else they offered (besides expensive water and caviar). I don't remember what all the costs were, but I think our meal overall cost $400 with the extras, and we tipped a total of $200, $150 for the Server and $50 for the Sommelier. But then again, we are, I don't want to say "high maintenance" because we are very easy to please, however, we savor everything possible, the wines, the cheeses, the apertif, etc. We were there far longer than anyone else that night because we took our time to enjoy the meal as that was our "entertainment" for the evening.