Ahhh...one of my favorite topics.
First, and foremost, before you can decide which list is most appropriate for you...you must come to grips with what you value in a golf course. Why? Because each list is derived differently and has a different set of criteria that they require their panelists to grade.
Golf Digest...is the oldest and most famous of the lists, most likely due to the fact that Golf Digest has the highest circulation of the Big 3 magazines. Key defining characterisitcs of the Golf Digest criteria are: resistence to scoring and shot values. Therefore, I conclude that difficult golf course might score more highly with the Golf Digest lists. Also, there is a general sense that Golf Digest favors beautiful layouts.
Golfweek...is the most robust of the lists and they break out their lists by era (modern, post 1960; classic, pre 1960). In my mind, one of the defining characterisitcs of the Golfweek criteria is the "Walk in the Park" item. This seems to lend itself to favoring natural and minimilistc golf courses.
Golf Magazine...isn't really a checklist rating system, like Digest and Week. They hand pick "elite" level golfers and have them select their favorite/best golf courses. They then compile the aggregrated list. The key defining characteristic of Golf Magazine is the phrase; "we don't tell our panelists what constitutes greatness in a golf course. They tell us."
For further information, I have compiled a list of what I call "Controversial Courses". This is a list derived from each of these Magazines Top 100 lists* and it details the courses which were only ranked by one of the rating entities. This lends itself to highlighting the courses which are favored by each magazines set of criteria (potentially).
http://www.mrpgolf.com/controversial.htmlPerhaps these lists can help you decide what your "go to" rating entity is.
*Yes, I used a aggregate Golfweek Top 100 US list. I know you aren't supposed to do this, but I did to keep each list at 100 courses.