First, a word on Advantages/Disadvantages
In general I think these things are great, and they're a good way to help define a character. The disadvantages a character takes will help the Player define the character psychologically while telling the GM what kind of trouble/problems that the player wants to face with that. If the player takes a phobia for example, at some point (or points) in the game they want it to come up. If they won't kill, they want to be put into a situation where killing may be necessary. Etc, etc, you get the idea.
The point here though is that mechanically you get points for taking these flaws, you pay points for getting those perks. The player will try to apply his perks all over the place, but not as many players will try to bring their flaws into play. That is where you come in though Mr. GM, bringing those flaws in. It is only fair isn't it? That flaw is how they paid for a mechanical benefit. At the same time though, if a player isn't using one of their advantages, bring it up a bit more for them. Remind them they have that nifty ability on their sheet. Use it. Use it for good, use it for evil, but use it.
Lastly, the whole theme of this is a 2 part sentence. "A good player will find a way to make their disadvantages advantages, a good GM can make an advantage a disadvantage"
That being said, lets take a look at some advantages.
Light Sleeper - Light Sleeper is one I see a lot of players take, after all you only need to ambush them in their sleep once to make a player want to be able to know when someone is coming in to kill him while he sleeps. Light Sleeper is generally pretty cheap too, while very strongly mitigating a key vulnerability everyone has, sleeping. However, being a Light Sleeper isn't all sunshine and roses either, remember that you can't just turn off your perception, especially when you sleep lightly. Any movement or noise in the camp/area can wake them up, they're as likely to wake up when an ally comes near them as when an enemy is. If they're on a battlefield, or somewhere new and strange, they're likely not going to get very much sleep. Their body will wear down with exhaustion as sleepless night after sleepless night hits them. Eventually they will collapse, or turn to something to help them sleep. At which point, you own them.
Ambidexterity - This one is another common one, particularly in fantasy games where melee combat is still pretty common. Also generally fairly cheap, all it does is let you use your off hand for free. Not much you can do to hurt someone with that now is there? Well, not exactly. Ambidextrous people are rare, and if someone knows that the man they're looking for is ambidextrous this can be the key to properly identifying them. Something as casual as throwing a water bottle and letting a PC who is pretending to be right handed, catch it with their left (since with ambidexterity their mind shouldn't be favoring a side being able to use both equally) and voila, your villain knows something that was trying to be hidden. I doubt their list of enemies has all that many ambidextrous people on it either.
Perfect Memory - Perfect Memory is a personal favorite of mine. I love playing the characters that can remember everything they see/read. Being able to use your notes as an IC reference and ask the GM if you remember key details (while pointing out your memory is perfect) can be a lot of fun, and help out a lot. The problem is though, you remember everything perfectly. See something traumatic, you're going to remember it every detail of it for the rest of your life. Nightmares and flashbacks are going to haunt you longer and clearer than most people as you just can't get that memory out of your head. As a player with this in one of my games said, "What has been seen, can never be unseen"
Meek/Harmless - You've seen this one before at some point I'm sure. You take an advantage like meek or harmless on your combat monster, and it means no one expects you to be the combat monster. At least not in a first meeting. You look harmless, and so you're rarely one of the first people attacked. Thus letting you explode onto the scene once the surprise rounds are done and teach those goons the folly of their ways. The trick to 'hurting' someone with this one is to remember meek goes both ways. Put them in a situation where they don't have access to their weapons, in fact weapons are limited and the NPCs aren't going to just give theirs up. Those NPCs, especially if they're cops or soldiers trying to protect the unarmed people are also going to be constantly in that meek PCs way, after all they look helpless. If anyone needs their constant attention, supervision, and protection it's that PC.
Magic Immunity - This one is a bit trickier, especially as some systems make this a conscious decision. That being said, if the player can willingly lower their magical immunity you'll need to wait for a time when they're unconscious. However, for those systems that just say you're immune to magic, or can't be targeted by spells. Don't forget, that means helpful spells as well. Unless the advantage specifies otherwise, a person whose body rejects magic is probably going to reject that helpful healing/detoxify spell just as much as it is going to resist that poison or magic missile spell. They wanted immunity to magic, I say give it to them. The good and the bad, the divine and the arcane. Magic is all about balance after all, isn't it?
this one is more for players, but looking at some disadvantages and some ways to use them as advantages, or at least slightly advantageous. It's not going to be as clear cut, because this is very situational and as a player you have less control of the situation.
Driven - There is a disadvantage like this in most games, basically you have a driving goal, there is something you just won't give up on. You will sacrifice anything for this goal, and when taking steps to accomplish this nothing is beyond you. Care should be taken whenever taking this disadvantage because it flat out kills characters dead. However, you can use it also. Your character has something that they will sacrifice anything for, that is spelled out in the disadvantage right there. As such, if something is hindering your progress that takes a will power check or sacrifice to get through, you should have a bit of an easier time of it. After all, failure means losing a shot at this goal right? It's not definite, but if you want to kill person A, and the only way to see him is to hold out under torture for him to come into the room, well what is a little pain and suffering right?
True Love - Another one, though I've only seen it in Legend of Five Rings. True Love is a disadvantage that means you put the actions of one person above everything else unless you can make a very specific test to resist it. Well, that sounds like a good way to resist seduction and bribe attempts doesn't it? I mean, provided you can make a direct link to succumbing to the seduction and making that person upset with you, or failing them in some way.
Dependant - This is one of the cheapest advantages that will either get you killed, or make a case that you're roll playing, not role playing. After all, you are supposed to care about your dependant. They're important to you, and you can be attacked through them. However, depending on the dependant they should also have friends, contacts, other people you can go to. People that are maybe not directly connected with you. An aging parent/grand parent probably has old friends with houses you may be able to hide in. A child has similar things with the homes of their friends. While you're watching over them, you can use them too. Watching people in a park is a lot less creepy when you are watching over your kid, or walking around with an elderly person. Bringing "junior" or "Grandma" to see "mom" in the hospital can also get you past some nurses desks pretty quickly too. If nothing else you can use them as a small distraction. Sure you'll pay for it later, but if you need another person right now, why not ask them to help?
the point I'm trying to say here, is basically the same point I am always trying to make. You can't just leave things in a game where they are specifically mentioned as applying. This is more than a game, it is telling a story, these people and the things that make them have more impact than just "spend 2 points to gain +1 to attack rolls" or "gain 2 points, but you have to feed grandma". Think about what you took on your character sheet, think about what it says about your character. Look at those traits, the good and the bad, and expand them to their logical conclusion. Your dependent might not be able to help themselves very well, but their must be something they can do. After all, they're not always with you right? Nothing, absolutely nothing in this world, or any world really, is 100% all good or all bad. There is another side to everything. You just gotta be looking for it to see it.