If you DON'T need to use the playstation 2 backwards compatibility don't get the metal gear solid bundle...
you can get the game cheaper used.
I think thats the only significant benefits there are
"Both the 80GB and 40GB PS3 models come standard with Cell Broadband Engine™ (Cell/B.E.), Blu-ray Disc™ (BD) player, built-in HDD, 1080p high-definition output, Wi-Fi connectivity and SIXAXIS™ wireless controller.
In addition to the larger HDD capacity, the 80GB model focuses on offering the incredible graphic quality, stunning gameplay, improved audio and visual fidelity that PS3 games are known for by maintaining the PlayStation®2 backwards compatibility through software instead of hardware. The 40GB model does not have PS2 backwards compatibility, although does maintain backwards compatibility for original PlayStation titles. The 40GB PS3 has 2 USB ports, where the 80GB PS3 has 4 USB ports. In addition, the 40GB PS3 does not have the multi-media memory card slots. Consumers can use a variety of after-market accessories for transferring their media to PS3 via the USB ports. "