I decided that if the cake is 3 layers, the size cut at the base would be skinnier, so I went with the Wilton wedding cake chart. I know they are for 2 layer cakes, but the pieces are 1" at the base. I figure that is the closest I could come to figuring it out! (I generally assume people cut 1.5" or 2" pieces out of 2 layer cakes.)
The surface space of the cake is the same (it's still 8" across the top). So the slices would be cut the same except they would be 6" tall instead of 4" tall. The customer is getting 50% more cake in each slice, so your per-slice price should be 50% higher.
Example:
1x2x4 = $3.00/serving (8 cubic inches - industry standard)
1x2x6 = $4.50/serving (12 cubic inches; 50% bigger than 8 cubic inches)
how to cut a wedding cake into 1x2x4 pieces: http://www.cateritsimple.com/id10.html
If you tried to cut a 6" tall cake into 8 cubic inch slices, you'd have to cut them into slices that were about 1.3" side instead of 2" wide. (1x1.3x6). That's one long, skinny piece of cake! About the size of a cake pillar!
If doing a 6" slice, find out what size plates they are using. A 6" slice of cake on a 6" dessert plate might have some overhang and doesn't look attractive.
I recently figured out that determining a per cubic inch of cake price was easier than a per serving size price.
So, if you get a request for a taller cake, you only have to calculate the change in size of the cake, not the number of servings.
For example, if you normally charge $2 per 1"x2"x4" serving (the Wilton wedding serving) that works out almost the same as 25 cents per cubic inch of cake.
Instead of having to go and figure a new number of servings or a new price for 1"x2"x6" servings, the price per cubic inch would be the same, you just have more cake to charge for.
Say you have an 8" round cake that you normally make 4" high. That's 200.96 cubic inches of cake (radius squared times pi time height ---> 4 squared times 3.14 times 4 ---> 16 x 3.14 x 4 = 200.96) for your standard cake, and for the "tall" six inch high cake, it's 301.44 cubic inches.
At 25 cents per cubic inch of cake, you get a price of $50.24 for the standard height cake and $75.36 for the tall cake.
Personally, I find charging this way is much easier than doing a per serving charging because the rate is the same no matter the serving size. It actually gives more flexibility -- you could have a chart showing different numbers of servings based on the serving size, so if someone is having a "cake and punch" party and wants to do larger pieces of cake, they would want to order more cake and you already have all the math done.
I hope this isn't too confusing written out like this. I'm currently working on a new matrix using this new pricing schema and once it is complete I will post it. I have emailed CK for data on the new pan shapes, too, so it will be a more complete matrix than my previous one, but still in the very easy to read MS Word table format. 
Okay.... looks like I might need to freshen up my trig and calc skills!
Heh, I cheat. 
Google is my friend. 
http://www.mathsteacher.com.au/year9/ch14_measurement/18_cylinder/cylinder.htm
Links at bottom of page for area/volume of all sorts of shapes.
And when the interweb doesn't provide the answer, doesn't hurt that DH and all his friends are math geniuses ...love that I can call or email any of them with a math problem and ZAP! they can solve off the top of their heads! I highly recommend EVERYONE have at LEAST one math geek friend! 
so are they wanting 3 layers, or you just want the cake to look taller?? I use 1/2" thick foam core under my cakes and do 2-2" layers with filling in between and the cakes are always somewhere between 5 and 6" tall. You figure 4" of cake and almost an inch with the 1/2" foam core and the filling. Maybe you could just charge like normal for a 2 layer cake and boost the cake up with some foam core. I ice all the way down the edge of the foam core so it's seamless with the side of the cake
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