I know this was a Voyager trick, but i'm a big fan of beaming in a chunk of antimatter and then standing back watching the cube go away. It just amazes me that our heroes routinely walk around the Borg... meet the Queen... and don't have a grenade-sized antimatter bomb to leave behind, on, oh say a transport time+3 second timer.
Antimatter is -really- powerful in very small quantity. The magnetic bottle technology looks very mature. And while maybe you can figure out how to protect a ship exterior, the interior of ships, and people, certainly can't deal with that type of explosion.
Remember the Doomsday machine? "Pure anti-proton" and it could cut through planets.