When ceiling mounted, indoor Access Points offer 360 degree coverage (omni directional) which is generally what people want for a data deployment however there are two main reasons why you may wish to use deploy an external antenna:
1) Altering the angle of coverage - For example, you may have a corridor that you mount an AP at on one end and use a semi-directional patch antenna to direct the signal down that corridor. This will enable areas not normally covered by an omni-directional antenna to be covered.
2) Power / Sensivity - Each AP and antenna both come with their own 'gain' values measured using dB. By using an external antenna, installers can get a higher power (so it will reach further) and/or a higher sensitive so the AP can 'hear' signals better from the clients. This is sometimes a little risky in terms of coverage because you can blast a signal a long way (100-200m) but your client may not have the power to get its signal back, creating a one-directional connection.
Useful antenna guide:
http://www.cisco.com/c/en/us/products/collateral/wireless/aironet-antennas-accessories/product_data_sheet09186a008008883b.html
What I've outlined above is a very general overview of the way some of the antennas and variables work. In reality it requires a bit of testing or site surveying to ensure you get the setup right depending on your requirements, device types and frequency used.
Ric
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