So far, I've only had a good experience at BIC Camera. I only have a glimpse at LABI and Yodobashi, no experience at AEON and so far, Amazon also has cheaper items, yet buying online has a lot of risks. As for BIC Camera, I like their points system for it has bigger percentage.
One time, we're able to buy a washing machine with the points we got when we bought a refrigerator. It was really a great deal!
When I was in Japan, I lived kind of close to Akihabara. I bought my camera at Onoden, went some times to Sofmap and a lot of tima at Yodobashi to get different items like a tripod. If I had to go to only one it would be Yodobashi, it's full of amazinf stuff.
My trick was to check the price on Amazon, then walk around in Akihabara, check the price. If I could get a good deal in a shop in one of the small streets, I would go for it. Of course, depending on the items (video games) I was also checking second hand at Book Off or other similar stores.
I usually stick to Labi, Bic or Aeon. Labi and Bic because they have outlet stores in Ikebukuro that are across the street from each other so it is easy to compare prices and even haggle a little as they are outlets. Aeon for the rest as I have a Waon card and all of my purchases get me points which turn back into money.