I recall a discussion on DoomWorld's forums going into this topic, actually. Somebody raised a pretty good point about how linearity sort of works on two levels - a macro scale (the game as a whole) and a micro scale (individual parts of the game in question).
Something like Doom is linear on a macro scale (you will always go through the same order of levels, with the optional secret stages always placed in the same spots) while less linear on a micro scale (obviously most maps are designed with a specific order of completion in mind - ie, find red key, open red door, find blue key, etc. - but the areas behind each door in the better-designed maps have a decent amount of space to explore, with not all of it directly leading toward the exit, but other bonuses and goodies). Likewise, the first Deus Ex fits into that pretty well (it's always Liberty Island -> Battery Park -> Hell's Kitchen -> LaGuardia Airport etc., but how you progress through that linear selection of levels is very open-ended).
On the other hand, they cited something like an Elder Scrolls game as open in a macro sense (I mean, it's an open-world game, kind of goes with the territory), and more linear in a micro sense (a lot of the various quests have a fairly strict linear progression - I'm not so sure I agree with this, since although my experience with Elder Scrolls games has been rather limited, I'm pretty sure there's some room for differing approaches to them).
Something like that exaggerated "modern game" would be linear on both counts (the game would progress the same no matter how you play it). Not entirely sure what open on both counts would be - Minecraft or something?
