MelonbooksDL: I don't have much personal experience with it, since the large majority of the music sold on it is (poor quality) MP3 files, which I'm not really interested in, even if there is bonuses such as scans.
My main complaint is the complete lack of any quality control, some files are WAVs with great scans, are files are untagged MP3 128k files with no scans. You also don't know the quality until AFTER you buy it, you can "guess" the quality by looking at the file size on the page, but it's not entirely accurate, obviously.
Booth.pm: Fairy good for the most part, I mostly use this to order actual physical CDs, which it is VERY good for. It allows you to order physical merch directly from the artists, it's basically a Japanese Bandcamp in that regard, which is very convenient.
One of the problems I have with it is the same reason I dislike MelonbooksDL, there is a lack of quality control for the digital downloads. Booth is MUCH better than Melonbooks in this regard, I find quite a lot of albums contain some form of lossless, but it's 100% possible you will buy an album and it will just be poor quality MP3s, and there is no way to see this BEFORE you buy the album.
It seems to "ecosystem" on Booth is more aware of lossless though, so I find the majority of stuff I buy on Booth does come in lossless, so it's not really a huge issue, but it's somewhat of an oversight.
Bandcamp: Can't really complain about anything with it, it should be the textbook example of a good online storefront, they offer both digital (in basically any format you could ever want), and physical goods, sold directly by the artists, takes a minimal cut (compared to other storefronts). It's just all around good. Unfortunately, there is a severe lack of doujin artists on it, compared to the last 2. It seems PayPal really isn't an convenient option for most doujin artists to bother with.
I haven't really used any of those other sites, since as far as I know they only offer lossy files which I'm not really interested in for the most part, and there's not really much on them that I'm interested in anyways.
I think the only other site I've used is DLSite, which is pretty much the same as MelonbooksDL (the site format is even very similar).