I hesitate to write about these as they are "secrets" after all... ;) (I love my little places!)
Little Shop Curry (Japanese curry to be exact)
It's a small, 14-seat shop run by a husband and wife duo that is only open 11:00 - 14:30 Mon-Sat. If you get there when they open, you'll wait in line. If you get there early and get in when they open, you'll still wait for food as they make every plate of curry as it's ordered. There's only one pot of curry for the day so they may close early (earliest I've seen them cut off the line was at 12:30). They have five choices for your curry, but really, you only ever need to order 気まぐれ (or set C, or as I like to translate it "whimsical curry"). If meat isn't your thing, then they do have a veggie-only curry as well. But assuming you're a C-set sort of person...
Let me walk you through the above. In the fore you see several juicy, freshly fried pieces of kara-age (Japanese-style fried chicken). To the right you see atu-age and hijiki, or fried tofu and a type of black seaweed respectively. Resting on top is a bit of grilled pepper and to the right, falling towards the curry is grilled egg plant. To the back left are several strips of tonkatsu, or fried breaded pork, and just peeking out from behind the tonkatsu at the back lip of the bowl is medamayaki, or a sunny-side up egg. This picture is a bit old, but they have now added some fried cabbage as well.
The picture doesn't really give you a size reference... but it's huge. I struggle to finish. In fact, most people I have taken there have struggled to finish.
Heck, here's another picture - a bit more intimate.
Pardon my drool.
The best part about this? It's only 700 yen. (If for some reason you just crawled your way back to civilization after being stranded on some uninhabited island for months on end, you can always get oo-mori [large portion] for an additional 100 yen. Then again, eating that much food after nearly starving probably isn't good for you... It would be best to order sukuname [the 'u' between the 's' and 'k' is almost silent], or small portion [of rice - you still get all the fixings]).
Little Shop Curry is located in the backstreets of Shibuya. But don't worry, I have you covered. Here's a map from Shibuya Station (https://maps.google.com/maps?saddr=Shibuya+Station,+%EF%BC%92%E4%B8%81%E7%9B%AE+Shibuya,+Shibuya-ku,+T%C5%8Dky%C5%8D-to,+Japan+(%E6%B8%8B%E8%B0%B7%E9%A7%85%EF%BC%88%E6%9D%B1%E4%BA%AC%EF%BC%89)&daddr=%E6%9D%B1%E4%BA%AC%E9%83%BD%E6%B8%8B%E8%B0%B7%E5%8C%BA%E5%86%86%E5%B1%B1%E7%94%BA10-15&hl=en&ie=UTF8&sll=35.658517,139.701334&sspn=0.020991,0.042272&geocode=FRUbIAIdVqxTCCmRweOJV4sYYDGX0uHSsN7amA%3BFf8dIAId1ZBTCClRi3JSqowYYDEfsiBzE0hmeA&dirflg=w&doflg=ptm&mra=ltm&t=m&z=17).
CHUBBY
No, I'm not describing you after eating at Little Shop Curry (though...). CHUBBY is my favorite cafe in Tokyo, though it's definitely out of the way. Located at Daitabashi Station (代田橋駅) on the Keio Line (京王線) - it's not JR - heading west out of Shinjuku, there's little chance you'll be "passing through" (unless you're headed to Mt. Takao at the very end of the line, which you can also access by JR).
CHUBBY is an art cafe where every month they feature a Japanese artist's works, whether they be handmade watches or pastel paintings. In fact, I first ventured to CHUBBY to see an exhibition by my favorite Japanese artist. The cafe has lots of space, but unlike many cafes you find in Jiyugaoka (自由が丘), it isn't crammed to the max with tables. In fact, they could probably easily fit another 5-10 tables in there... (they only have 6 as it is). While a few of the 2-3 person tables have chairs, the other tables seat you on couches - deep, comfy, couches (actually a bit too deep at times considering the height of the tables).
The fare at CHUBBY is a mix of Western and Japanese, though my favorite dishes include the Pumpkin Gnocchi, Rosemary Roast Chicken, Stewed/Boiled Pork & Daikon (煮物), Hayashi Rice, and usually, whatever their monthly menu item is (they also have a daily menu item). There is usually only 2, maybe 3 people working so it takes awhile for food to come, but it's never really busy. Another reason why it takes awhile for food is that they make it as it's ordered. It feels like you have a personal chef! What has always amazed me is the huge selection of dishes CHUBBY offers. Their food menu is a good 8 pages long at least and yet everything comes out perfectly (trust me, I've eaten nearly every item on their menu). Combine that with a doubly long drink menu and you have yourself a nice relaxing evening with friends lounging in couches, gazing at art, and consuming delicious food & drink.
I went so often that they knew me immediately whenever I called to reserve for a large party (Japanese only).
Au Temps Jadis
While I've never been to France to try truly "authentic" galettes and crepes, I must say that ATJ makes the best galettes and crepes I have had in Japan. Located in the area between Harajuku and Shibuya (both places notable for their crepe stalls), ATJ is a sit-down restaurant geared toward the more refined crowd (or those who don't mind spending a bit more for mouthwatering galettes and crepes).
ATJ is perhaps the hardest restaurant to find among these three. Don't worry a map is below. Their galettes range from 1000Y to 1500Y while their dessert crepes range from 600Y to 1000Y. My personal favorite crepe is their banana chocolate (or their hazelnut chocolate...). Add a dollop of vanilla ice cream and you're in heaven.
But before that, if you want a light meal you can always try one of their galettes.
All this in a quaint, dare I say, cute basement shop that is nevertheless lit by natural light.
ATJ is closed Wednesdays, but otherwise open every day until 7p. It's always busy on the weekends during the day, but it tends to slow down in the evening.
Here are those promised maps from Shibuya Station (https://maps.google.com/maps?saddr=Shibuya+Station,+%EF%BC%92%E4%B8%81%E7%9B%AE+Shibuya,+Shibuya-ku,+T%C5%8Dky%C5%8D-to,+Japan+(%E6%B8%8B%E8%B0%B7%E9%A7%85%EF%BC%88%E6%9D%B1%E4%BA%AC%EF%BC%89)&daddr=%E6%9D%B1%E4%BA%AC%E9%83%BD%E6%B8%8B%E8%B0%B7%E5%8C%BA%E7%A5%9E%E5%8D%971-5-4+%E3%83%AD%E3%82%A4%E3%83%A4%E3%83%AB%E3%83%91%E3%83%AC%E3%82%B9%E5%8E%9F%E5%AE%BF&hl=en&ie=UTF8&ll=35.663241,139.700443&spn=0.005247,0.010568&sll=35.661765,139.700795&sspn=0.010495,0.021136&geocode=FRUbIAIdVqxTCCmRweOJV4sYYDGX0uHSsN7amA%3BFf8zIAIdI6hTCCEBA6HGrENcDA&dirflg=w&doflg=ptm&mra=ltm&t=m&z=17)
... and Harajuku Station (https://maps.google.com/maps?saddr=%E5%8E%9F%E5%AE%BF%E9%A7%85&daddr=%E6%9D%B1%E4%BA%AC%E9%83%BD%E6%B8%8B%E8%B0%B7%E5%8C%BA%E7%A5%9E%E5%8D%971-5-4+%E3%83%AD%E3%82%A4%E3%83%A4%E3%83%AB%E3%83%91%E3%83%AC%E3%82%B9%E5%8E%9F%E5%AE%BF&hl=en&ie=UTF8&ll=35.66753,139.700754&spn=0.010494,0.021136&sll=35.663241,139.700443&sspn=0.005247,0.010568&geocode=FZhIIAIdn7FTCCkXDTTIuowYYDEz2UVvrkmwjg%3BFf8zIAIdI6hTCCEBA6HGrENcDA&dirflg=w&doflg=ptm&mra=ls&t=m&z=16).
Maruichi Bagel
Bagels in Tokyo? Like, non-bread legit bagels?
YES.
But you'll pay a bit... (a lot). First let me tempt you:
Now that I (hope I) have your attention, that right there cost me about 1300Y. (I was excited to see a blast from the past - Martinelli's Apple Juice - and couldn't resist, I think that itself was about 500Y).
Maruichi Bagel has a good variety of bagels from the standard fare (Blueberry, Egg, Poppy, etc.) to the health nut bagels (think flax seed, whole wheat, oatmeal etc.). What you see above is my own creation of tofu & fig cream cheese (so good!), smoked salmon, tomato and lettuce in between a blueberry bagel.
I was so excited to find good bagels that I also purchased a bagel with red bean and sweet potato salad as the stuffing (it was savory, not sweet!). Needless to say, they're not stingy when it comes to the fillings (I couldn't get my mouth around it... [cue Kat Li]). So, if you find yourself in Tokyo and in need of a bagel, definitely make your way to Maruichi, which, like everything else on this list, is a bit hard to find. The nearest station is Sirokanetakanawa (白金高輪駅). As usual, here's the map (https://maps.google.com/maps?saddr=%E7%99%BD%E9%87%91%E9%AB%98%E8%BC%AA%E9%A7%85&daddr=%E6%9D%B1%E4%BA%AC%E9%83%BD%E6%B8%AF%E5%8C%BA%E7%99%BD%E9%87%911-15-22&hl=en&ie=UTF8&ll=35.644917,139.733273&spn=0.005249,0.010568&sll=35.66753,139.700754&sspn=0.010494,0.021136&geocode=FRfeHwIdWCxUCCnRXvuuqYsYYDFUWpWLBojVFw%3BFfPnHwIdEihUCCl_Sk_hp4sYYDH8YZMiFBY-Tg&dirflg=w&doflg=ptm&mra=ls&t=m&z=17). It's also a pleasant mid-morning walk from Roppongi/Azabu-juban (walking directions: https://maps.google.com/maps?saddr=Tsutaya,+Roppongi,+Tokyo&daddr=%E6%9D%B1%E4%BA%AC%E9%83%BD%E6%B8%AF%E5%8C%BA%E7%99%BD%E9%87%911-15-22&hl=en&ie=UTF8&sll=35.644917,139.733273&sspn=0.005249,0.010568&geocode=FeYbIAIdACRUCCG0AjCEBAzWQQ%3BFfPnHwIdEihUCCl_Sk_hp4sYYDH8YZMiFBY-Tg&dirflg=w&doflg=ptm&mra=ls&t=m&z=15)
Well then, I hope I have sated your interest in little Tokyo treasures but stimulated your appetite. Eat on!!