There is no foolproof way to find the secret room (except with some of the items you can pick up, like x-ray glasses), but 99 times out of 100 you can find it with one method and a little luck.
Most secret rooms are contained in between at least 3 other rooms. All you have to do is look on your minimap for 5 rooms that are all joined in a square "U" shape (3 on the bottom, and 2 for the sides). Bombing in the middle of the wall that faces towards the gap in the U from any of the 3 rooms that will share walls with the room will lead you in.
You can then bomb your way out into another room if you so choose. This can be useful in getting into the treasure room with no keys if the secret room borders the treasure room.
Some maps have more than 1 "U" shape in them, in this case you're just going to have to guess and hope to get it on your first go.
Some maps won't have even 1 U shape, in this case, the room will probably be in bordered by 2 other rooms, so look for a set of rooms in a square "r" shape and hope that the one you picked is the right one.
The super secret room (Wrath of the Lamb DLC only) is found in a different way. The super secret room will NEVER border more than one room (except very rarely the regular secret room).
To find the super secret room, look for any walls where if there was a room on the other side, it would have no other entrances, similar to the treasure rooms and shops.
Unlike the secret room, the map (or the tarot card "The World", or any similar items) won't show the super secret room. X-ray glasses and the Spelunker hat will still work however.