I have been in SD on business from the UK about 8 or 9 times and played golf pretty much every time. Here is my take:
Torrey Pines: A disappointment (both courses). Just not very interesting - I remember very few holes, and as for pace of play, a calendar is more useful than a watch.
Aviara: Expensive and well kept. Moderately interesting, but by no means a must-play.
Maderas: This is actually my favourite in the area. Interesting holes, playable but challenging.
Meadows Del Mar (and several other names): Also an interesting layout, has been in good condition every time I played it. Not cheap.
Steele Canyon: Canyon 9 very good, Ranch 9 OK, meadow 9 dull.
Auld Course (now renamed): Nice enough and fair value, but never a links no matter what John Cook says.
Singing Hills (Scyuan): Out of tune, if you ask me.
Rancho Bernardo Inn: Nice enough, but nothing special. OK if staying there, not worth a trip.