From the Myst serie, to me Riven is the best one :
exploration, amazement of the wonderful settings,
and puzzles that are all ultra-logical and yet sufficiently
complex and with hints spread over the maps so that it is understandable.
Considering a dungeon crawler, I like the last version of Conflux a lot :
with a reasonable party (at least 2 characters) it's quite balanced,
with a lot of freedom, a host of puzzles, strange places
(like the sewers and their ecosystem, with plants spreading, monsters etc.)
What lack the most are more friendly creatures and a dialog system.
The dungeon itself is also very big and stuffed with so many things that
are here only for the challenge... It is always better to keep things within
a coherent universe.
One thing that I also would advocate :
adding a class of creatures that have the same characteristics as players.
Why :
- They could provide a bigger challenge than the average creature
- It would allow dialogs / situations to convince those creatures to join the party as in "Ishar" or (maybe) "Might and Magic", and also leave it.
- It would be more realistic
- It would be a step toward a MP dungeon
Actually the best PC RPG to take influence from are Fallout 1 & 2.
So even if they are not dungeon crawlers, they have everything
a player should look for : atmosphere and design, freedom of choice,
coherence and causality of the universe (with quest having an influence
on the environnement), multiple possibilities to solve a problem
(more than most player would think of).