Portal - Limitation on what surfaces a Portal can be opened on.
Because it would offer no challenge.
Fallout - Humour.
Its a satirical deconstruction of mid 20th century ideas of the future with a whole bunch of cultural references and a healthy dose of fatalism. Take out the humour and its a deconstruction of mid 20th century ideas of the future designed to inspire wrist slitting.
Peggle/Casual games in general - The Sound effects.
Go play a casual game with the sound off, or better yet with a horror game soundtrack in the background. See what I mean?
Startrek games - the Crapness.
Because a decent startrek game strait out of the box would not actually require modding... ..and where's the fun in that?