While I disagree with most of the WotC article, this bit struck me as pretty sound conceptual advice:
However, I'd add the caveat that while making level that is "bullseye" shaped on a conceptual/flowchart level (a la Melan's graphs in the OP) is a good idea, it's lame to make the map literally bullseye-shaped. it's much more interesting, I think, to have broad/long "high traffic" corridors that connect various sections of the dungeon/level with few, if any, "decision points" in-between, and then complex mazes of winding corridors and rooms that "fill in" the intervening space -- so the most 'remote' section of the dungeon (in terms of decision points and intermediate encounters/'challenges required to reach it from the 'start' point) might actually be physically very close to the start point -- which can cause interesting situations to arise with "treasure finding" spells and/or magic items (the players will know a great treasure (or great magic, or great source of evil, or whatever they are "detecting") is located close by, but not how to get to it (which is also an ideal "organic" plot hook -- find a way to get to the treasure/magic/bad guy/whatever that we already know is there)), makes spells like passwall more useful -- allowing the players to shortcut from point A to point Z (or vice versa) without necessarily having to pass through points B-Y (the author of the WotC article would presumably disagree with my assertion that this is a desirable possibility, but, well, I already said I disagreed with most of that article...), and also incentivizes players to make more careful and accurate maps so that they will, for instance, realize when they're approaching the area that their locate object spell had told them the treasure/whatever was in, or that they're in an area where a passwall or similar magic could allow them to make a quick retreat to the surface.
which, I would point out, pretty closely parallels some advice Gygax and Arneson gave way back in 1974 (D&D vol. 3: The Underworld & Wilderness Adventures, p. 6):Rather than start the PCs at one edge of your graph paper, put that first entry staircase in the middle of the map. Drop them into a room that gives three or four choices right off the bat, and your players will revel in the choice. Then, build your dungeon like a bullseye, with easier encounters near the middle of the map and the tough stuff tucked away at the edges and corners. Include periodic branches, especially ones that connect within the same “ring” of the bullseye. Now the players perceive meaningful choice, and you know the PCs won’t get to the corners without the prior experience they need.
In laying out your dungeons keep in mind that downward (and upward) mobility is desirable, for players will not find a game enjoyable which confines them too much. On the other hand unusual areas and rich treasures should be relatively difficult to locate, and access must be limited. The layout of a level will affect the route most often followed by players. Observation of the most frequently used passages and explored rooms will guide the referee in preparation of successive levels, which, of course, should be progressively more dangerous and difficult.
However, I'd add the caveat that while making level that is "bullseye" shaped on a conceptual/flowchart level (a la Melan's graphs in the OP) is a good idea, it's lame to make the map literally bullseye-shaped. it's much more interesting, I think, to have broad/long "high traffic" corridors that connect various sections of the dungeon/level with few, if any, "decision points" in-between, and then complex mazes of winding corridors and rooms that "fill in" the intervening space -- so the most 'remote' section of the dungeon (in terms of decision points and intermediate encounters/'challenges required to reach it from the 'start' point) might actually be physically very close to the start point -- which can cause interesting situations to arise with "treasure finding" spells and/or magic items (the players will know a great treasure (or great magic, or great source of evil, or whatever they are "detecting") is located close by, but not how to get to it (which is also an ideal "organic" plot hook -- find a way to get to the treasure/magic/bad guy/whatever that we already know is there)), makes spells like passwall more useful -- allowing the players to shortcut from point A to point Z (or vice versa) without necessarily having to pass through points B-Y (the author of the WotC article would presumably disagree with my assertion that this is a desirable possibility, but, well, I already said I disagreed with most of that article...), and also incentivizes players to make more careful and accurate maps so that they will, for instance, realize when they're approaching the area that their locate object spell had told them the treasure/whatever was in, or that they're in an area where a passwall or similar magic could allow them to make a quick retreat to the surface.