For web apps you can set the startup screen with apple-touch-startup-image
What about for iPads?
I only got the startup image to work by making a PNG image with dimensions of 748x1024. This was tested on an iPad with firmware 3.2.1.
Portrait image needs to be 768x1004 (note: 1004, not 1024, 20px is for status bar), PNG is the preferred file format.
Landscape image needs to be 1024x748 (note: 748, again 20px for status bar). This image then needs to be rotated 90 degrees clockwise, end result is 748x1024.
Link tags in header need to be as follows:
<link rel="apple-touch-startup-image" href="images/splash_screen_768x1004.png" media="(device-width: 768px) and (orientation: portrait)" />
<link rel="apple-touch-startup-image" href="images/splash_screen_1024x748.png" media="(device-width: 768px) and (orientation: landscape)" />
For the new Retina iPad (if you don't add these, it will use the above with pixel doubling):
<link rel="apple-touch-startup-image"
href="images/splash_screen_1536x2008.png"
media="(device-width: 1536px) and (orientation: portrait) and (-webkit-device-pixel-ratio: 2)" />
<link rel="apple-touch-startup-image"
href="images/splash_screen_2048x1496.png"
media="(device-width: 1536px) and (orientation: landscape) and (-webkit-device-pixel-ratio: 2)" />
Previous answers (including the accepted answer) at time of posting this didn't work with my testing.