(Protoss and Jungle Basin are used as examples throughout the answer)
But the problem is that usually good player will 100% prevent "late" scouting with SCV.
That's why I send my scouting SCV early.
If you do so, you should be able to run around his base and then if he doesn't follow you can hide at his natural, in a corner or go back to the XN Tower. If he does follow you you might want to consider coming back home, or just lose the unit...
What can I pay attention too?
You should pay attention for Gas, what buildings he does have and what buildings he doesn't have.
Let's say we scout Protoss, if he doesn't have Buildings, something fishy might be going on.
If we scout that he has 1 Assimilator and 1 Gateway, he will probably throw down a Core soon...
But I don't know what units he has after my initial scout?
Placing your scouting SCV in a location that gives you easy access to his base again, allows you to check his base again to know what units, composition and technology he goes for.
Does he have more Zealots, more Stalkers, or missing some? Robotics? Stargate? Templar?
But my scouting SCV is dead so I can't do this.
You will suggest to use scan. BUT. Usually Terran has 2 CC+OC that are usually used for MULEing. Yup, you shouldn't be greedy and spend some energy for scanning...
I would rather spent energy on a scan to see my opponent planning to warp DTs than suddenly having them in my base right after I did a MULE because "I thought he would attack with Zealots and Stalkers". But instead he produced less of those, thrown down Cannons at his wall, warped them in...
The first energy is wisely used on a MULE to get the OC cost back, it would be too early after your last scout to gain enough additional information which would be a waste. But let's look at the second time you get energy to use your OC for scouting purposes, this looks like the ideal time to throw down a scan to reveal more...
If you really have to, you could opt to create a Flying Scout Rax or send in a Marine.
But those might give you less or too late information...
What about expanding?
the 1st thing to do - is check expansions: if player started expanding or not yet... ok. that's fine and easy to do... but then:
After the above info, would you still check for an expansion first? You should be able to figure out based on your scouting if he might have opted for a Fast Expansion, you might not know where, but it will probably be his natural, others would be hard to defend and more easily scouted with a Hellion.
What about players hiding production facilities?
But the higher level players usually hide there production facilities. Moreover, too often they keep SOMEWHERE army. That is not on the base choke, that is not close to MY base choke...
If he would hide one of his first production facilities (Starport), you should see that his armies are smaller because for every Void Ray he bulds his army will have less units. If you suspect, it's important to get some kind op map vision at key locations.
Take a look at Jungle Basin for example. If you were the top player, where would you hide your technology? Not at the right side of the map, my opponent will see your productions right away when he comes to attack you. Instead, you would run out your base with your Probe and run straight to the left, go upstairs and start building a Starport right there.
A Terran player would only see that when they planned a Medivac drop at the Mineral Line in your Base, but by then you have Void Rays to take out the Medivac and attack something right after. Some Terran players might see that when they patrol around the map, or check that place for sure if they need their third expansion there...
How can you remedy that? Patrol a Marine between that spot and the third expansion and you will know two things at once: Is there a Proxy in the top section? Does he goes towards my backdoor?
Other than revealing cloaked units, what can I still use my scanning for later on?
and often my scanning show almost nothing....
After winning some aggressive play on the middle of the map, you decide to back-door your opponent. Obviously, you don't want to reveal to him that you are doing so and that's why you scout the place where he most likely would be gathering his army to know his composition and to trick him into thinking that you would attack that spot instead. Let's hope he doesn't see you break the rock...
Another situation would be that you see his army defending his third expansion at the side. So as an harass you go for a drop with a small army in his base to take out some Pylons, if your lucky this requires him to take a big portion of his army back from his third expansion to protect his production.
And there you go, you set up your next army to raid his third expansion. Do a last scan to check if his army is manageable now and go for it. If not, pull back and do another harass, enjoy... :-)