Defeating the Cavern Boss:
Use Time Changers wisely. Use Pause when he is just normally attacking you to get behind him easily, and when he does his two-charge attack. When he starts to charge at you in the two-charge attack, use Pause quickly and move out of the way (unless you can dodge it). Another way to avoid his two-charge attack is to use Record. When he starts charging you the first time, use Record and run around. He cannot hurt you, and when you return to normal time, he will follow the recorded version of Blinx instead of the real version. An easy way to hit him without using time alterations or waiting for his normal charge is to shoot any piece of junk at him when you are relatively close. When he sucks it in, run behind him and shoot him.
Defeating the Forgotten City Boss:
Use the water in the middle. The Boss for some reason cannot go into the water. If you are in there, you can get to the correct location and hit him from behind.
Defeating Deja Vu Canals Boss
When you are in Deja Vu Canals boss level, when you start, collect trash and then walk through to the area. When the boss appears, run to the right and you will see a ledge, jump on top of it and you will be safe. Remember to only shoot at him when his back is turned to you.