Almost all PDFs that are used to create a physical publication use the CMYK or RGB colour profiles.
However, Apple devices (iPad/iPhone/iPod) only support Apple RGB colour profile. This means that the PDF colour profile will need converting to the correct type. If the PDFs colours are not converted to the correct profile then the colours on the page will appear different to the PDF being viewed in Acrobat.
Here is a side by side comparison of an publication viewed on a iPad - one PDF has not been converted to Apple RGB whereas other one has.
RGB and CMYK Colour Profile
There are two ways to alter the colour profile of a PDF. The first is to edit the file when exporting to PDF using InDesign (this method will be added to the wiki soon). The second method is to use Adobe Acrobat Pro.
You can click the following links to download the profiles for use in Acrobat that will be discussed in this guide:
Acrobat 9 Profile Acrobat 10 Profile
How to import the profile
Acrobat 9
Advance > Pre-flight > Options > Import Pre-flight
Acrobat 10
First you must ensure that Print Production is available under Tools. To do this, click the drop down panel just under the Comment section and select the Print Production option:
To then import the profile, select:
Tools > Print Production > Pre-flight > Options > Import Pre-flight 
How to use profile
Now that the profile has been imported it will appear under the Imported Profiles subheading - simply double click the profile and select a save location for your newly converted PDF file:
Benefits of using Pre-flight
Adobe Acrobat Pro has a standard tool that allows you to alter the colour profile of a PDF. We recommend not use this as the tool seems to increase the file size of the PDF while the above profile reduces the file size by a considerable amount which means less for the end user to download.