The best practice is to use PNG files as often as possible when using images within your app. iOS and Xcode load and display PNGs quickest as opposed to any other type of format. If given a choice, go with PNG.
When you use any other file type (or if you load a non-optimized PNG files), your iPhone has to do the byte-swapping and alpha premultiplication at load-time (and possibly re-do the alpha multiplication at display time). Your application basically has to do the same processing that Xcode does, but it's doing it at run-time instead of at build-time. This is going to cost you both in terms of processor cycles and memory overhead. One of the reasons why Mobile Safari is the biggest memory hog of the built-in iPhone applications is because the images it has to load in order to display web-pages are all non-optimized images, mostly JPEGs. Since JPEG is a compressed format, it has the added extra step of having to decompress the image into memory before it can do the premultiplication and byte-swapping.