Best courses in San Diego:
1. Barona creek
Super fun course and IMO the best design of any place in San Diego county. Every hole is unique and challenging. Greens roll fantastically and the course is always in impeccable shape. Another big plus is that it's usually completely empty. Greens fees will prob run you like 60-100 bucks depending on when you play making it the best bargain in town if you want a top notch course without breaking the bank. Only downside is that it is way off the beaten path, prob about 30-40 min from downtown sd.
Sick course. Very hard but has like 7 different tees so noobs will be fine. It's a troon golf course so it's always in impeccable shape but that def comes at a price because a round will cost you 125 -225 or so. Definitely the most challenging greens in San Diego
3. Torrey Pines South
Greatest course ever if you're a resident because you can play it for 40 bucks. Not so sweet when you come out of state and pay 225. This course is more about the location rather than the design of the holes. You pretty much have to play a fade off every tee. This course will definitely rape your face but it does it with length and ridiculous rough. If you're not a really long hitter you will probably be hitting three wood into a couple par fours. What the course lacks in design it more than makes up for in scenery. The views of the ocean are nothing short of stunning. Just make sure you do your homework before playing...sometimes the course is in less than ideal condition which sucks if you're shelling out the non resident rate.
Nice Arnold Palmer course up in Carlsbad. It's always empty and in fantastic shape but it'll cost you one or two hundred bucks to play. Well worth the money though IMO
5. Torrey north
All the beautiful scenery of south for almost half the price. Also it won't crush your soul as badly. Very fun course.
6. Steele canyon
This place is a great bargain. 27 holes and the moves rolling greens of any public course I've ever played. You can get on for 50 bucks usually if you book online.
7. The crossings
Nice course up in Carlsbad. Like 80 bucks I think.
Three courses you can play out here. One is an executive. They're nice layouts, usually in good but not fantastic shape. Greens fees are really cheap though which is nice if you're on a budget.
This is pretty much the ultimate noob course in San Diego. If you must play it, play early in the morning. If you don't you will have a five hour round guaranteed. Always packed with hackers and tourists. It's always in very good shape but the layout is a little uninspiring. You can drive the ball all over the planet and not get in trouble but the greens can be impossible to get up and down on if you miss in the wrong place.
10. Carlton oaks
This would've been way up on my list a couple years ago but unfortunately the course has lost its greens. It might still be worth playing though for 30 bucks. They design of the course is unbelievable (it's a rare public dye course). The tips are absolutely unreal and a PGA pro would be hard pressed to hoot under par. I think they clock in at 7400 yards or so. IMO its easily the hardest course in San Diego.
Hope that helps