even games that require third party applications, emulation, and in many
cases, community designed patches to run?

whine about steam, and forget all those hundreds of old games that
simply wont run without special effort and software. i'm sure you'd have
no trouble throwing them on a list.

I personally don't think SS2 deserves to be on this list but at least it
qualifies to be in consideration given that I can install it and play it now
whether or not Irrational is still in business and running a validation
server.

Since HL2's lifetime is by design constrained to the business lifetime of
Valve and their willingness to validate the game online, it's automatically
disqualified for any "All time greatest game" list I'd consider
authoritative (it's also automatically disqualified from any game purchase
list I'll put together.) In order to pass the "all time" test, you have to
be installable and playable for "all time"!

If Valve should someday deign to put out a downloadable, archivable,
offline-installable patch that frees HL2 from this umbilical, then we can
talk.

just so noone misunderstands me, I dont think Doom 3 will be on such a
list, but Half-Life 2 will absolutely be on the list.

Maybe Doom 3, but not Half-Life 2

http://www.gamespot.com/features/6130956/index.html

In a couple of years time NOBODY even remembers the shitpiles like Half
Life 2 or Doom 3.