I like a 1x5 with an ogee bed molding on top. It ends up about 5-1/4" tall. It's easy to miter and cope and I think they look a little better than stock base moldings. It's my preferred method unless the customer or architectural design dictates otherwise.
I've seen 2-1/2" colonial casing and other window trim used as base. It always makes me queasy.
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Asking how tall the trim should be is like askign what color the walls in your living room should be, the answer is: whatever height/size/style *you* like the looks of, after all, you are the one who is living in the house so don't buy baseboards based on what someone else likes, or what some claim is the current "style" this week.