OK, I have been preferentially planting heirloom vegetable seeds for the last few years, but this year, after an eye-opening tomato discussion on heirloom vs. hybrid vs. open pollinated genetic diversity, I'm having second thoughts.
I have to say I AM confused, however. In this context, what does an "heirloom" apple tree mean, exactly? Since most apples need to be cross pollinated (Adams County Nursery has a large pollination chart on-line that I find useful), and by practice, are not usually grown from seeds, I doubt it has the same connotation as vegetable seeds. Then, there's that treatise on apple cultivation in The Botany of Desire
My usual apple variety recommendation is to look for disease resistant cultivars based on prevalent apple diseases in your area.
I have Enterprise, Pristine, and Arkansas Black. Enterprise is a semi-dwarf tree. Pristine and Ark Black are being espaliered. Although I haven't actually purchased from ACN above, here again, they have a lovely system of specific disease resistance scores assigned to each cultivar they sell.