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Backwards Compatability
Backwards compatibility is the ability of a game console to play video games developed for previous iterations of the console. In the Playstation 3's case, its list of backwards-compatible games consist of Playstation and Playstation 2 games. Though both consoles feature some backwards compatibility, the 80 gb model of the PS3 has major issues running games from previous consoles. The reason the 80 gb model has issues running older games is because the console uses emulator software rather than the Emotion Engine chip that the 60 gb model uses, which runs more games with better quality.
Cost
At most major retailers in 2009, the PS3 80 gb model costs $299.99. The PS3 60 gb model, however, costs $319.99 and higher at most websites that sell them. The reason behind the 60 gb model costing more than the 80 gb is that Sony discontinued distribution and production of the 60 gb model in 2008. As a result, they're in much higher demand and harder to find.
Hardware and USB Ports
While the 80 gb model has the obvious extra memory, the 60 gb model has four USB ports compared to the 80 gb's two in some models. This difference in USB ports can limit the amount of USB-enabled accessories and tools that can be used when operating your PS3.
Availability
Due to the discontinuation of production of the 60 gb model, it won't be found in most major retailers. Even when available, the store or website you find it at may only have a pre-owned or refurbished console. The 80 gb, however, is available almost anywhere video games are sold, and usually comes bundled with other games for free.
Determining Which To Choose
The 60 gb and 80 gb have minor differences, but these differences can be crucial to how you use the console. If your main need for the console is video games, and you own Playstation 2 games, it may be best to find and purchase the 60 gb console. If you're more likely to use your PS3 as a Blu-ray player and web browser, the 80 gb model may be just right for you.