Just got back from a tour of Croatia and Slovenia. When you're near the coast the seafood is the way to go. Once inland the food becomes comfort food similar to German cuisine--gravy, meat well done, stews, etc. Here are some restaurants that I liked. Prices are in US dollars, two people, a starter or salad and an entree, a liter of table wine before tip (which is around 10%):
Hotel Rixos/Libertas--20 minutes from Old Town. Dinner buffet. Outstanding! $100 but if you back away they may cut the price in half. Beautiful seafood salads.
Lokando Peskarija-on the waterfront behind the city hall. $60. I had whitebait and my wife had mussels in wine broth. One of the best meals if you like to eat little fried fish whole.
Proto-The best meal for both of us. $95. I had seafood risotto with squid ink and my wife had octopus stew. Great!
Atrium Hotel (Cardo Restaurant)-beautifully decorated restaurant in modern style. $65. I had veal roll and my wife had shrimp onm arugula and mozzarella. Lovely meal.
Istranka-$55. Veal in a wine sauce and my wife had an octopus salad followed by calamari. Not overly breaded but very tender.
Yacht Club-$55. My best meal of the trip--squid a la Opatija--squid on sliced potatoes with a light tomato-based sauce. Outstanding. My wife had grilled vegetables.
Kaneta-$55. A ton of roasted lamb--the lesser parts so cooked thoroughly. A lot of fat but thoroughly enjoyable. More than you can really eat. Great service.
Kvarner-actually in Lovran about 6 miles from Opatija. $70. I had the seafood brodetta (fish, mussels, squid, octopus and shrimp in light tomato based sauce)
Gostilnapri Planincu-$60. My wife had pork with a mushroom sauce and I had a pork cutlet, breaded as big as your head. More than I could eat. Comfort food to the max.
Union-$65 We both had the House meat plate. More comfort food and plenty of it. We should have ordered the lamb chops which looked great. Fabulous service.
Sokol-$70. I had mountain oysters and my wife had veal stew. Beautiful restaurant. Wild game is their main thing.
Vinodol-$50. I had the cold meats plate and my wife had pasta with truffles.
Boban-$40. We both had great pastas. In the cellar of an old building owned by a former professional basketball player. Lots of local celebrities/jocks.
Ivica i Marica (Hansel and Gretel) in back of the open air market. Beautiful interior with antiques. $60. I had beef goulash and my wife had fried bread with cottage cheese/sour cream. (I know this sounds a little strange but it's a classic for Croatia--they specialize in traditional foods.) Great restaurant.
Hope this helps. We wold recommend any of the above restaurants. I haven't bothered to mention the ones we didn't care for.
Next time you are in Zagreb, try Pod Grickim Topom, off the Upper Town (Gorni Grad). Great local cuisine in a very pleasant setting. And yes, Zagorje cuisine (north central Croatia) is derivative of the Austro-Hungarian culture that once dominated the area.
If you are lucky enough to visit Sipan, try to get into Konoba kod Marka. Probably one of the top 5 lunches I have had in my life! Also, in the Old City of Dubrovnik, try Renaissance (in the evening) and Marco Polo. I personally was not wild about Proto... too commercial for me.
We've just come back as well. Some of our favorite meals and one stay-away recommendation:
Dubrovnik: The Hotel Bellevue was our "finest" dining experience and about $140 with wine. We ordered a la carte, but they also offer a 4 course set menu. We shared local Ston oysters, I had a beef dish wrapped in prsut (Croatian prosciutto), husband had a veal dish with the most delicious mushroom risotto (risotto is ubiquitous in Croatia).
The best octopus salad we had on our trip (and we had many) was at Konoba Kamenice.
Also try the D'Vino wine bar for a good introduction to Croatian wines.
Mostar, BiH: Konoba Dvije Pecine (Restaurant Two Caves). A charming location near the little bridge with wonderful home-cooked food. Our best meal in Mostar during our two night stay.
Hvar, Croatia: Luviji. This place is two restaurants. A nice restaurant upstairs with terrace dining and a regular menu. And a cosy, tapas style place downstairs. We opted for the tapas style. Only two choices: the peasant plate (mostly meat based) and the fish plate, for about $16 each. We ordered one of each and a buffet of small, traditional foods followed. Washed down with wine from the family's vineyards. Total bill about $45. This was one of our favorite places and a great chance to try a number of local foods. Too bad we didn't have time to try upstairs.
Antika in Stari Grad on Hvar Island had great food. A more inventive and deftly prepared menu than most other places. We tried house made anchovies, a rocket salad with fried cheese, and a shrimp dish.
Luna: Stay away!! I decided on Luna for our last night in Hvar, rather than the nearby Zlatna Skoljka. The latter was excited about their food, eagerly describing their "challenge" courses (you pick seafood or meat and the number of courses; they do the rest). But I decided I didn't want such a big dinner and Luna had a lovely terrace. Bad choice. We were going to try the local fish specialty "gregada" (fish stewed with potatoes, etc). The couple next to us was not enthusiastic about this dish, so we splurged on the "lobster lunatic". A whole lobster with a pasta and tomato/wine/brandy sauce. I could make a better dish at home. We paid over $100 for an overcooked lobster and unmemorable pasta and sauce that barely fed both of us. Oh, Zlatna Skolkja, why didn't I choose you?
Also, Prsut Tri is another excellent wine bar. They're very helpful with wine information if they are not busy.. A few specialty nibbles including prsut (of course), cheese, and kulen, a spicy sausage from the slavonia area.
Also, check out the wine "tasting" restaurants on the islad for the Zlatan winery and Tomic winery. While they don't do a typcial tasting of all of the wines, you can order wines much more cheaply by the glass than found eslewhere and eat as well. We ate at the Zlatan location - on the water, good food mostly prepared in front of you in an outdoor facility. A little on the pricey side, but the wines (direct from the source) were a great value. And you can swim off the side of the restaurant.
Istria: Konoba Mondo is great and has friendly, helpful service. The NYT called it the best restaurant you'll never get to, which I think unfairly raises one's expectations. It is a typical Croatian Konoba (but with a focus on Istrian truffles), with simple cooking and normal hits and misses. But we had a good dinner of teran wine, tagliatelle with truffles, a rumpsteak with a wine and truffle sauce, eggplant salad, dessert and coffee.
Bled, Slovenia: Okarina. Wow. This was one of our favorite restaurants. Strange menu covering Indian food, pastas, and Slovenian dishes, but really good. Good service, good wine, etc. The Indian food smelled so appealing, but we tried the typical Slovenian dishes (a roe-deer stew, and some local mushrooms over polenta), the best avocado dish I've had in my entire life, and their version of the Bled cake. The last was very good, but it was not really a Bled cake.
Also, we stayed at tourist farms during our Slovenian stay and had great food at both (Skerlj in Krast area, and Psnak in the Bled/Triglav area). Some of the best and most consistent meals of our trip.
Zagreb: I would second Ivica i Mariska, despite it's kitchsy feel. The spinach and cheese strukli is oustanding. Vinodol also good. We reserved earlier in the day so that we could secure the veal baked under a pot dish. Wish we could have gotten a reservation for the 5-table Prasac. Finally, we were so excited to have Thai food at a place called Opium, right next to our hotel (Arcotel Alllegra). Such an exciting change for our taste buds. Despite it's location in the basement of a shopping center, it seemed to be quite the Zagreb date spot.
Last eve we wandered by chance into Marley & Me, http://www.lunchcafe.si/, less than a ten tables in the old town of Ljubljana. Fairly simple fare reminiscent of Trieste, well prepared, non-pretentious, good, and they actually served vegetables :). It is on my list of places to which to return, and I had given up on any place in Ljubljana making my list.