Tyler (26 mo) recently went through a phase of this after he was sick. We've also seen it here and there out of the blue when he was younger. Our number one rule is no binky throwing. He's old enough to understand it, and if we let him do it, it becomes a game to him. When he throws it, we'll go in, look him straight in the eye, and tell him "Binky stays in your crib. If you throw it, mommy will take it away." We'll say it a couple of times to make sure he understands and give it back. If he throws it again, we take it away and tell him "mommy said binkys stay in the crib. I'm going to take this away until you can keep it in the crib." Yes, he goes bananas and screams the house down, and I feel incredibly mean, but it curbs the binky tossing. He either falls asleep without it or gets it back after he calms down.
We've had great success with the "in and out" method. After the routine, we put Tyler into the crib, even if he protests. We have a key phrase ("night night, Tyler") that we say, then we leave. We stand in the hallway and give him a few seconds to settle himself. We count to 10, some people count to 5, it really just depends on your DS and how long it takes you to realize that he isn't going to soothe himself. This is different from controlled crying because you don't increase the intervals and you LISTEN to your DS to determine when to go back in and soothe him. When he doesn't settle, you go back in to him. We start with standing outside the door and say our phrase (night night, Tyler). If that doesn't work, we'll stand in the doorway where he can see us and say it again. If it still doesn't work, we go to his side and say it again. As SOON as he calms down, we leave again and start over. This can go on for a long time, and you'll likely be in and out of his room billions of times. But if you're consistent, it does work. It may take a little longer, since you've tried some other approaches that may have reinforced his fear, but stick with it!
The point of all this? If he's afraid of the crib or having a bout of sep anx, the key to him getting over it is knowing that if he cries, you respond every single time. Lots of parents on the site have had success with this...I'm sure you'll hear from them too! Good luck and let us know how it goes!