Well, a number of dangers in mines...
Critters, collapsing supports, exploding gasses, falling rocks, tripping and falling onto hard surfaces, breathing in large quatities of small dust, entrapment, drowning, tools breaking suddenly on veins of stronger material and possibly flying into your face..
I would agree with other points made in this topic, in regard to 'hiding minerals'. Having bits of rock in front of certain veins which can be removed, would add for more of a search. Hitting certain 'false rocks' might trigger one of many dangers.
An ore which is hanging over a support might be critical to the structure's stability, and could bait the greedy ones into their untimely demise. Some parts of the cave system may be underwater, and require some diving and the like, to reach. Give mines more of a maze/labyrinth feel through larger layouts, with more complex, but thinner'n smaller tunnels. It would likely increase the atmosphere of discomfort. Also, a mine should probably have more than one entrance or exit.. And not all must be artificial.
In regard to minecarts... They shouldn't make it too easy to get around the mines. And they shouldn't connect the entrance to the rarer minerals. While a long minecart ride can be 'epic'... There's lil' roleplay involved, and lil' actual mining. It could be useful in mines were all the common minerals near the surface are depleted, and a deeper level is present to mine said 'common-minerals'...
But, other than that, I wouldn't really know.