There are several tiers to Cocoa-based interfaces. Generally, I recommend working at the highest level of abstraction that meets your needs for presentation and performance.
The base UIKit elements that you can place using Interface Builder or code are designed to handle the most common cases within an application's interface. These provide some degree of customization, depending on their type, but what you see is generally all you get. On the iPhone, Apple even tries to maintain a certain look and feel for these stock elements by rejecting applications during review that use them in ways that contradict the Human Interface Guidelines.
The next level down are custom UIViews. These can be made to look like anything through the use of Quartz drawing within the -drawRect: method. You can do your own touch handling by overriding methods like –touchesBegan:withEvent: or by using the new UIGestureRecognizers. Given the level of customization you can do here, this is where most people stop when tweaking their interfaces.
You can go a little lower than this by working with Core Animation layers and animations. You don't gain a lot, performance-wise, by using CALayers instead of UIViews on the iPhone, but they can be useful if you want to craft visual items that use the same code on Mac and iPhone. Custom animations may be required if you want to do something more than animate a view between two states linearly. You can even do some limited 3-D work using Core Animation.
Finally, there is OpenGL ES for display of full 3-D scenes and for really high performance graphic display. This is about as close to the metal as you're going to get when dealing with the iPhone display system, and it shows in terms of the amount and complexity of code you have to write. For complex 3-D work, this is what you will need to use, but for 2-D and even rudimentary 3-D I recommend looking first to Core Animation because of the code it can save you. If performance is unacceptable, then should you go to OpenGL ES.
Now, just because you need to use one of these technologies to work with part of your interface does not mean that it can't coexist with the others. UIViews are backed by Core Animation layers, and even OpenGL ES renders into a CALayer which can be placed in a view. Again, use the highest level of abstraction that is appropriate for that part of your interface.