I read through the first three pages looking for my favorite spots to be mentioned, saw a couple were, many weren't, and realized that most people aren't reading this whole thread anyway so I'll just throw them out there again.
Top Five Bars
1)
The Frying Pan (Spring/Summer Only, 26th St and the Hudson River) - It's basically a couple of boats docked just above Chelsea Piers, they serve Corona by the bucket (6 in a bucket for $36 I think), and they have a grill. I love drinking by the water, so chilling on the Hudson and drinking Corona is a good way to spend a day/night. It gets crowded, so get there early on nice Fri/Sat nights or do some day drinking on the weekend on a nice day.
2)
Bohemian Hall & Beer Garden, aka "The Old Beer Garden" (24th Ave and 29th St, Astoria, Queens) - There's an indoor and outdoor section, but you want to go during the summer and sit outside. On weekend nights you may need to get there a little early to get a table. The food is good, go for a brat or a sausage, and the beer and atmosphere are great too.
3)
Death and Company (East 6th between 1st Ave and Ave A, East Village, Manhattan) - It's near a cluster of bars over by Tompkins Square Park, but you can walk right past it and miss it. The huge, wooden front doors are not really marked, but you'll see a doorman outside, well dressed usually, and possibly a few people waiting. They'll only let you in if there is open seating, there is no standing in this bar. It's sort of a prohibition era feel inside, although it's not quite a speakeasy, with all of the bartenders wearing three piece suits and serving up expensive, but wonderful cocktails. I like to stop in here and have one or two drinks a few times a year. The reason for the name? During prohibition, supporters of the Volstead Act said that to drink was to "live a life shadowed by death." Those who drank anyway would sometimes sarcastically toast to "Death and Company."
4)
PDT aka Please Don't Tell (St. Mark's place between 1st Ave and Ave A, East Village, Manhattan) - This one is only a few blocks above Death and Co. and is a similar place. They're both tough to get into on weekend nights without a reservation, so sometimes I'll head to the area and gamble on one or the other having space. If not, there are plenty of other bars around there to kill an hour wait. You can easily miss PDT if you don't know what you're looking for. You have to go into a hot dog shop (Crif's Dogs) and look for a phone booth on your left, likely with some people milling around it. Walk in, pick up the phone and they'll answer on the other side and let you in or take your name. The wall opens up into a door and you're in. Inside the feel is similar to Death and Co, but slightly less upscale. You can also order hot dogs from Crif's, which get passed through a hole in the wall. Last time I was there, on a first or maybe second date, the date saw Scarlett Johansson in the corner and didn't tip me off. Terrible job by her.
5)
The Garden at Studio Square, aka "The New Beer Garden" (36th St near 36th Ave, Long Island City, Queens) - Don't let the LIC address scare you, this area is more or less considered part of Astoria. This is a bigger, newer, cleaner version of the original, with less of that old world feel. The beer selection is awesome and they have some cool events. Last summer I went to a pig roast there with David Burke serving up some cool dishes at a reasonable flat rate price, all you could eat and drink.
Restaurants
I'm a bit of a foodie, but on a budget, so I can't speak to some of the high end places... But, I have been to some unique spots, so I'll list those.
1)
Les Halles (Multiple Locations) - This is Anthony Bourdain's old place, he's still listed in name only, but I doubt he stops in very often. Regardless, it's a meat lover and steak lover's paradise. It's also cheaper than you'd expect, IMO. No dish is more than $30, except those that are servings for two. The Planche de Grillades is a great sampler, with lamb chop, hanger steak, merguez, steak, thick cut bacon,french fries, and provençal dressing. It's $28 for one, $56 for two. I liked everything but the merguez, and the steak (sirloin, I believe) was my favorite. I've gone with the sirloin on all future visits, but the thick cut bacon is always missed. There's a french beer on the menu that's pretty good, too.
2) Kabob Cafe (Steinway St and 25th Ave, Astoria, Queens) - This place was actually featured on Bourdain's Outerboroughs episode and it's a 10 minute walk from my place so I had to check it out. Ali is the chef and it's all Egyptian food. It's only got four or five tables, and Ali will come and talk to you and explain what is on the menu that day. By menu, I really just mean he'll ask you some questions and give you some options. He'll ask you what meat you want (I think he has vegetarian options too), then make a suggestion. We always go with the suggestion and we've never been disappointed. He'll suggest a few different dishes to go with it, it's family style servings, and you can pick and choose. It is a bit adventurous (we tried duck testicles last time we were there), but 90% of the things I tried were delicious. He'll also explain the cultural significance of some foods as he brings them out, which is awesome.
3) Cafe Lalo (83rd St and Amsterdam Ave, Upper West Side, Manhattan) - This is the cafe that was in You've Got Mail, when they're waiting outside for the blind date setup. It's a great dessert spot, with probably about 200 different dessert options on the menu. The regular foods are pretty eccentric, with a lot of healthy options and some different/random ethnic offerings. They supposedly have great coffee too, although I can't vouch for that. It's a great spot to take a date for dessert, because girls probably like that movie and it's also not too far from a park where you can walk along the Hudson (although that walk is a little creepy at night, because you don't walk through parks in NYC at night...).
On my to do list over the next few months is trying some different Chinese spots in Flushing, which I hear has more authentic Chinese food than the Chinatown in Manhattan. I also want to hit one of the top steak places - Peter Luger's or Wolfgang's... And I want to try some good Italian places. I really, really, really want to eat at Rao's, but it's literally impossible. 8-10 tables, one seating per night, Monday to Friday only and the tables have owners each night. Translation? You can call and call, but you pretty much can't get a reservation.