according to the Ball canning book (paraphrasing)...
JAM is made by cooking crushed or chopped fruits with sugar, and is made of one fruit or a combination of fruits, is spreadable, and is firm but will not hold the shape of the jar.
JELLY is made from juice strained from fruit, usually prepared in a way to keep it crystal clear, and is gelatinized enough to hold is shape when removed from the jar, yet is still spreadable.
PRESERVES are fruit preserved with sugar so it retains its shape, is transparent, shiny, tender and plump. the syrup generally has the consistency of honey, and a true preserve will not hold its shape when spooned from the jar.
to add to the confusion, i'll also add their descriptions of...
CONSERVES, which are jam-like and made of a combination of one or more fruits, nuts and raisins, cooked until it rounds up on the spoon.
MARMALADES are a soft jelly containing pieces of fruit and peel evenly suspended in a transparent jelly. similar in structure to jam.
This table comes from the front of the muffin section in Bread, by Beth Hensperger:
Muffin size Baking time Yield
Mini/gem (1 5/8") 10-15 minutes 18-20
Regular (2 3/4") 20-25 minutes 9-10
Oversized (3 1/4") 25-30 minutes 6-7
Muffin cake (8-9") 55-65 minutes 1
The baking times are for 375-400°F; most recipes will fall around that range. Note that the yields don't necessarily match up to typical pan sizes; for example, if you take a recipe meant for 12 regular muffins, you'll probably have more batter than you need for a pan of 6 oversized muffins. Perhaps this is your problem - you could be overfilling. If even after scaling the volumes appropriately, you still have problems, you could try reducing the temperature by 25°F and increasing the baking time.
("Muffin cake" refers to baking in an 8-9" pan of some sort - the author says that you can get away with it for any muffin recipe, but I've never tried it!)
Best Answer
There is considerable overlap between cupcakes and muffins.
Method
From a technical point of view, muffins are made by the muffin method, making them small quickbreads. In the muffin method, the wet ingredients are combined in one bowl; and the dry ingredients are combined in another bowl. Then the two are quickly incorporated together with minimal mixing to avoid gluten development. This gives muffins a somewhat coarse crumb.
Cupcakes are small cakes, and are made by one of the traditional cake methods such as the creaming method, the reverse creaming method, the genoise method, the chiffon method, and so on. They tend to have a finer crumb than muffins.
Contrast
While no single criterion distinguishes a muffin from a cupcake if you do not adopt the technical definition above, the following trends exist: