For buying things to take home for gifts and personal use, I almost always make a trip to the Aeon Laketown Mall in Saitama at the end of a trip to Japan. From the perspective of many foreign tourists, this seems like an odd suggestion, because essentially it is just a huge (really huge) Western-style shopping mall, and it isnft even in Tokyo. (It takes 45 to 60 minutes to get there, one way, from various places in Tokyo, but itfs an easy ride on JR, with only one change of train, and most of the time I am able to sit all or at least most of the way.) The thing is, I find it to be a very efficient solution for buying certain types of items, especially midrange snack items and other things that are best bought in a large supermarket. (There are actually two of them there, each with a somewhat different selection and lineup of brands.) There are a couple of decent-sized 100-yen shops there, a Muji, and a lot of other shops for food, tea, kitchen items, stationery items, and assorted other things, although the vast majority of the shops are devoted to fashion, accessories, and cosmetics (not things that interest me). For the things that I buy there, a single stop at Laketown is much less time-consuming than moving around to different stores and neighborhoods in Tokyo, and it is completely weatherproof (the JR station is right at the main entrance). There is also an outlet mall there, although I am not really an outlet mall person.
Anyway, itfs not for everyone, but I love the place and have always been grateful to the person who suggested it on a Japan travel forum years ago. So Ifll just put it out there, even though I know that the suggestion of going to a Western shopping mall will offend many Japanophiles. I typically spend four or five hours there including a lunch break (there are LOTS of restaurants there as well as casual eating possibilities), at which point I havenft even begun to cover all the stores of interest to me, but I do get tired. Add an hour each way for transit, and I usually get back to my hotel by midafternoon (I try to arrive at 9) with a big haul of great items. (To carry them back on the train I take a duffel bag and a backpack with me.) A real plus is that if you go on a weekday, it is almost never crowded. (Avoid Sunday afternoons, though!) Itfs no longer new, but it is well kept-up and comfortable (free lockers, lots of places to rest, good bathrooms). Itfs just on the huge side (you get your exercise for the day) and I wouldnft recommend it to someone with mobility impairment.
I also make time for a few places in Tokyo, my favorites being Tokyu Hands (I like the Shinjuku store best myself) and the basement floors of Shinjuku Takashimaya and Isetan (for high-end snacks). I will admit that Donki has a lot of good stuff at good prices, but I have just never liked the ambience at Donki, and it tends to be oppressively crowded. (My best experience to date has been at the Shibuya Mega Donki very early in the morning.) Also, a huge 100-yen shop is kind of a must, especially if I donft get out to Laketown. My favorite is probably the Daiso in Kinshicho, but there are several other good ones in Tokyo. (I wouldnft go out to Kinshicho from the Shinjuku side of Tokyo just for the Daiso, but itfs worth it from Tokyo Station or someplace like that.)