A few comments on your list:
Rolling 3d6 in order
The idea with this is "take what fate gives you and see if you can make it work." It's a challenge, which is part of the fun. In my experience, there's a different attitude when starting a 1st level PC "old school:" you start with a blank slate. You see what fate gives you. Then you start imagining, from there. Any background you give the PC is sketchy; a more elaborate background will come about through play...if he survives. You might roll up a backup 1st level PC "just in case."
This is a very different attitude and approach than the popular one, these days, where you envision the PC you want to play and *create* him, complete with background, et cetera. (In some cases, you even have an idea of his "destiny.")
I should also note that
ability scores weren't as important, originally.
Complicated and scattered charts and tables
Complicated? I wouldn't characterize them as such (although I'm coming from a white box OD&D point-of-view). Typically the PCs one or two charts that apply to them, and they can write down the column or row that applies directly on their character sheet, or just rely on the DM (who has the relevant tables at hand on his screen or in his DM Ref Sheets).
Weak low-level mages/powerful high-level mages
Leveling differently
I comment on the different power-curves in my
musing on experience and advancement.
Henchmen, hirelings, guard dogs, et cetera
This is certainly something that I associate with older edition play. Adventuring parties were often quite large. Henchmen provide a source of replacement PCs, in case of PC death. Hirelings (including men-at-arms) provide additional muscle, torch-bearers, and such. All NPCs provide a rich source of role-playing interaction and dynamism to the situation. Loyalty, morale, and such become very important considerations, especially if the NPCs are strong enough to start considering the PCs an easy source of instant wealth.
Regular Dying and PC replacement
I touched on this earlier. It's all about attitude and expectations.
DM vs. Players, not working with the players
Eh, I'm not really with you on this one. I think this is more of a caricature than anything. I think an old school DM's role is to act as a judge or referee: an impartial arbiter. In my games, I'm rooting for the PCs, but I play the monsters and present the challenges accurately and appropriately. However, when I play the monsters against the PCs, I still chuckle evilly when I make a good roll or pull off something nasty. Superficially it might *seem* like I'm a vicious bastard enjoying my attempts to kill them, but that's not the whole picture. I think a lot of the "DM vs. players" thing comes from this type of thing.
Clumsy pastiche of pop culture, pulp fiction, and mythology
Yeah, I guess. I wouldn't say that's necessarily an old school distinctive, though.
Simple Game, few options
Yes, although I'd say something like "fewer codified options/systems." Much more left open to DM adjudication. I don't find that a simpler system means fewer options in play, though. Again, there's something of an attitude difference, here. What the PC does (or can do) in a given situation comes very much from what the player wants to attempt, rather than a list of options on his PC sheet. And the DM has a lot of leeway to handle this or interpret it.
I don't consider these holes to be patched, or areas where new rules need to be applied. Rather, they're areas where rulings need to be made as individual situations come up.
Dungeon as an underworld, where every PC cannot see in the dark and every NPC can.
Sprawling, nonsensical mega-dungeons
This is a subject I talk about in my
musing on the dungeon as an underworld. I'm big on the concept of the "underworld," which goes a long way towards mitigating and explaining the "nonsense factor;" it provides a believable reason for the weirdness. Of course, not every dungeon need be a megadungeon or a mythic/mystical underworld, but I think most old school campaign should have one.
Wayne, your point/question non-humans already being able to see in the dark is answered in that dungeon/underworld musing I linked to, above.
Wilderness adventures
The thing about old-school wilderness adventures is that they were often "hex-crawl" type of things, where they PCs mapped out an uncharted wilderness, et cetera. The focus was on exploring the unknown. That theme of "exploring the unknown" is also very prevalent in old school dungeon play.
Invincible Overlord
I love Judges Guild stuff. The Wilderlands is probably my favorite published setting.
NPCs and PCs follow different rules
Yes. Here's my take: the rules for PC creation and advancement are there because that's central to the idea of the PC. PCs can be in the game a long time, advancing over that period; they benefit from a framework that guides their advancement and development. NPCs and monsters simply don't need to be built by the same set of rules. They don't need the advancement guides; they need whatever abilities and stats the DM wants for them to have. It needn't be explained in terms of PC rules; not everything in the campaign world is built on PC rules.
Several different parallel version of the game
Hah, yeah. My early games were a mix of Holmes and AD&D, with a few things from B/X and Holmes D&D making appearances at times, too. At the time, we didn't really draw big distinctions between the various sets of rules, although there are quite a few.
Everyone had house rules
Sure. I'm not sure that's necessarily limited to old school, though.
Okay, all that said, here's a few things to consider:
Challenge the players, not just the PCs
Touched on above.
A focus on exploring the unknown
Touched on above.
Let the players drive the story, and let the story develop through play
(Another aspect of this is letting the players go where they want. They should be able to go straight to the 7th level of the dungeon, if they want to. They should be able to go to the wilderness lair of Snagcatha the Wyrm if they want to. They shouldn't assume that they are on a track where everything they encounter is placed there with their general levels and capabilities in mind. This also made scouting very important. And also research and rumors about a particular site. You tried to see what was ahead of you, and you had to know when to run. And when you ran, you had to know how to prevent or delay pursuit. Hold portal. Wizard Lock. Iron spikes wedged under doors. Drop food. Drop treasure. Et cetera. All this is very old school.)
Rulings, not rules
Touched on above.
Heroic, not superheroic scale
PCs start of pretty weak -- barely more capable than the average man. Even at higher levels, they're never Superman. They're Batman.
Fewer XP for monsters, more more treasure (or goals)
XP for treasure is a story goal, where the story is "PCs seek fortune and glory." In old school play, you didn't get very much XP from combat, compared to the XP you got from treasure (the goal). This encouraged goal-oriented play. Wandering monsters were to be avoided, as they sap resources without having much treasure. Clever ways to acquire the treasure without fighting were always good. An old school approach rewards the goal. Killing the things is actually incidental...it's taking their stuff that's really important.