Can't speak to the brown cracks but the hole is probably a fruit worm. They are little dark brown worms avout 1/2" long w/ white or yellow markings. Pick off the plants and throw them out of the garden.
Watch out biting into tomatoes with the holes .....they stay inside!

Tomato fruitworm; see the pictures at the very bottom of the page:
http://www.mobot.org/gardeninghelp/PlantFinder/IPM.asp?code=286&group=22&level=s

Thanks guys! I was afraid of that. Does this mean I will have more of these guys? I'm an organic gardener, and check plants frequently, never seen any bugs on mater plants.

I discard any tomatoes with bug holes...even if it's not a fruitworm living inside the tomato, the hole can cause rot.

The cracks you describe sound like radial cracking, which is common with some varieties. The brown spots on the cracks could be rotten areas because contaminated rain or hose water can get into the cracks and cause rotting. (by "contaminated" I mean it can contain fungi spores, etc)