The only difference other than HDD size is that the 40GB model doesn't have backwards compatibility with PS2 games (all models play PS1 games however).
The 40 gig has no card readers and only two USB ports. There is no PS2 game support and there is no update or anything else to allow PS2 games to work.
The 80 gig has card readers and four USB ports. It also supports most of the PS2 games (could be around 90% or more by now).
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