Restaurants at which to buy wine. First, let me tell you about the restaurants that are genuinely friendly to wine drinkers.
My new favorite wine-friendly restaurant is Cuvee in Bird Rock in the south west of La Jolla. The food is superb, the wine irresistably priced, and the dining room is lovely. They have a really unique method of wine pricing. They charge below list price for their wines, and then add an $8 corkage fee on top of that. If you bring a bottle, you get the same deal, an $8 corkage fee. Their wine selection is excellent, specializing in blends. You can buy bottles there and take them home, which is a steal. They're promising to open a wine shop next door.
A long-time favorite is Trattoria Acqua in La Jolla (1298 Prospect, 454-0709), which puts a fixed markup (I'm told $10) on its wines. This means that you are getting a really good deal on the more expensive wines. I've also seen some rare--but affordable--wines on the menu, such as the Turley Zinfandels. They have an excellent mix of domestic and foreign wines, current releases and older wines. They have some interesting wines by the glass, but I haven't tried them. The food? Excellent mediterranian cuisine at an affordable price. At the low end they have individual pizzas starting at about $9. Pastas are also affordable, in the $12-$15 range. The ambience is nice, too, but try to get a table away from the major foot traffic.
You won't believe me, but Aesop's Tables in University City (8650 Genesee, 455-1535), a local Greek restaurant, is very wine friendly. They have a small wine list consisting entirely of affordable wines ($10-$25), and unlike most affordable restaurant offerings, these are good quality, the ones in the middle price range typically rating Very Good on my scale. Many of their wines are available by the glass (around $5), and they even have some half bottles. Their secret seems to be a combination of good taste and sensible markups. Bravo! The food is not haute cuisine, but it's very good, and the atmosphere is very friendly.
Restaurants to bring your wine. Many restuarants charge too much for wine or offer wines that I'm not fond of. One secret I've learned is that restaurants will let you bring your own bottles of wine, but they'll charge you a fee. I've been charged as little as $5, a bargain, and as much as $15, painful. You can often tell from the menu prices what the corkage fee is likely to be, but you don't have to take chances. Before going, perhaps while making your reservation, ask what the corkage fee is. Often we just bring a bottle of wine discreetly kept in a bag so that we can check out the wine list first and ask about the corkage fee. This leaves us the option of choosing a wine from the wine list if something is interesting or the corkage fee is unreasonable. Another thing to keep in mind is to choose your wine to match the corkage fee. Since markups tend to be double or more, I try to bring a wine that is at least as much as the corkage fee, preferably more. This way I know that I'm saving a little money and drinking a wine I'll like.
In my limited experience, the place with the lowest corkage fee and the best food is Barolo (8935 Towne Centre Drive, 622-1202). The food is great, the people really nice, and the corkage fee $5. Hard to beat.
An old favorite is Lorna's Italian Kitchen in University City (3945 Governor, 452-0661), charging only $5 and serving wonderful Italian food. Try the baked brie; it's divine!
Going by the glass. I frequently pay the $15 corkage fee at the more pricey restaurants, simply because their wine markups are even more outrageous. However, another approach is to buy wines by the glass. Many restaurants charge the same relative price by the glass as they do by the bottle. (You can check this by comparing the glass price of the wine to the bottle price; if the bottle price is 4-5 times the glass price, you're doing alright.) The problem is that some mid-range restaurants don't have very good wines by the glass. However, I've found a number of places do, including Laurel's, Montana's, and Wine Sellar and Brasserie. What distinguishes these places is that they are selling great wines by the bottle, so their wines by the glass aren't shabby, either.