Whew. This isn't as easy as you'd think. The short of the "cupcake" question is simple though: often there is no difference. Many big breakfast chains will serve you cake batter "muffins" in a heartbeat. A true muffin will be a bit coarser, a bit more bread-y. It's like the difference between a biscuit and a scone.
The basic muffin (oil,egg,milk,powder,flour) is easy. The problem is when you start mixing in flavor. For heavy stuff (pumpkin leaps to mind) you need to add more baking powder and baking soda as well. I also tend to separate my eggs, and fold in some beaten egg whites for a little extra lightness.
For berries and wet things, shake 'em in some flour first, so all the fruit doesn't settle to the bottom of the muffin. I'd shake them in the flour you plan on using for the muffins, so you don't get too much flour in your batter. If you're using frozen fruit, don't bother to thaw.
Sour cream, yoghurt, and buttermilk can all be subbed in for some of the milk. Thicker batter needs to have proportionately more leavening agent, while looser, wetter batter should have less (so as to avoid weird bubbles). There is no "right" consistency for muffin batter: some will be thicker and some will be thinner.
With subbing in different fruits and vegetables, the most important thing to consider is their water content. Berries are pretty much interchangeable. Apples and peaches, on the other hand, aren't. I'd rate a peach as being more like a berry in that sense (I used to go to a place that made peach and cream cheese muffins that were literally worth killing for. Literally.)