For me, it really comes down to experience, and just a tad amount of luck. Now, finding secret rooms is relatively easy. You usually focus on the empty spaces with a lot of adjacent rooms.
There are of course, those times where it seems like there simply isn't a place for the secret room i.e., you've exhausted all of the spots with 3 adjacent rooms, or there simply were none to begin with.
My guess for these types of floors, is that the Super Secret room must be the third room. Either this, or instead, the Secret room is only connected to 2 rooms. I'd however not attempt these types if I thought that the second were true.
If you're going to attempt to find the secret rooms on that floor believing that the first of the 2 ideas above, be mindful about whether the super secret room could indeed fill in any of the potential third slots.
On another note, if a Curse Room is adjacent to a secret room of any type, then a spiky doorway frame will connect the two.
Now, there are some things you can do to help as well. Try to trick your foes into doing the dirty work for you!
Note that the efficiency of this depends not only on your skill in dodging, weaving, and avoiding danger, but also on your level of patience.
If the enemies in the room always aim explosive shots at you, stand near the walls, and quickly move out of the way just before they shoot them. Repeat for all of the other walls if unsatisfied.
If any enemies in the room randomly shoot explosive shots with no regards as to who or what they hit, and are able to move (Walking Guts are an example, they're green versions of Boils), simply wait it out until A. You're certain that they had accurately hit the wall... or B. You no longer feel safe and comfortable prolonging this. The amount of explosive potential enemies you leave alive is determined by your level of comfort, but do try to limit their numbers to at least 3...
Lastly, you have Bomb Flies, Mulligoons, and to a lesser extent, Mullibooms. Simply wait until they approach a wall, and attempt to time their death so that they die and explode on the wall. A bomb fly can fly near any potential doorway given enough time, so be extra patient with this method. Mulligoons when killed, drop a Troll bomb, so if you're daring and quick enough, you can push this into a wall, if it might not seem close enough.
Then there are those Mullibooms... I however, have not intentionally led these types of enemies in the hopes of uncovering a secret room. I find that their pursuing nature, and instant explosions makes them a dangerous choice for this sort of action.
This is just about all I can suggest. I will remind you however, that this all really does come down to simple experience. The more you do this sort of thing, the more likely you'll accurately guess the location of any of the secret rooms. Consider this one important thing though... Never ever try to actively bomb open a secret room of any type if you do not have a great deal of bombs. Taking a guess now and again is ok, but don't waste 3 bombs if you only had 3 to begin with.
Understand that basic secret rooms, which are known for (but not limited to) carrying large amount of money), lose value once you enter the Womb, simply because A. All currency loses value starting from the Womb, and B. Because the most common drop in Secret Rooms is money.