I basically only use two brands of thread... Metro Pro thread and Floriani thread. I bought all 166 colors of the Metro 5000m spools when I began doing machine embroidery over 10 years ago. I love the Metro thread for it's ease of stitching, sheen, the fact that it is polyester and very inexpensive...a win win all the way around. I fill in colors I am missing with Floriani as they have a very vast color selection and extremely good blending shades in almost every color category... I store them by color in plastic boxes that lock and have a handle.

I use polyester embroidery thread from ThreadArt for Embroidery. Solid color, 1000m spools currently on sale for $1.89 each. Various size sets can also be purchased at a reduced price. Shipping is also very inexpensive--and the savings quickly off-sets the shipping costs if purchasing only a few spools. I also use their cotton threads for nearly all my general sewing.
https://www.threadart.com/

I pretty much do the same as dragonflyer/Kim. Occasionally if I only need black and white I order a thread called brothread from Amazon. It reminds me much of the Metro thread

I have all of the over 200 thread colors from Madiera. I've never had trouble with it so I figure if my machines like it, then I'm fine with it. I have sewing thread in a decent sized carry case, serger threads of various weights in a couple of plastic bins and drawers and embroidery thread in drawers. I try to keep all of my thread protected from dust and light.

Like AuntAnnie, I also use ThreadArt poly. We have different brands of embroidery machines and that thread works very well with both machines. also I have a set of Floriani thread and cannot tell the difference using the two kinds of thread except ThreadArt is more affordable. To avoid purchasing duplicate colors, I have made a spreadsheet with the thread listed in number order then cross reference with Madiera thread colors. As far as storage, The Floriani is stored in a plastic bin made for wrapping paper that fits under the bed, somewhat in number order. The ThreadArt is in individual sandwich bags on spool racks also in number order.

I have a selection of different brands of thread. The 1000m reels of thread are kept in a small chest of drawers in the unit my machine is on. I have threads for my PR stored in two or three large plastic covered boxes. Smaller reels of thread live in a plastic containers in colour groups. When embroidering I work out what I want for a stitch out and often its a selection of brands. I live a long way from my dealer so apart from when I bought the machine I am not tempted to go in and buy a reel or two when passing. Living in the UK buying from other countries in bulk gets pricy as we pay import duty on top of the cost of the thread. Also living where I do I make do with what I have. My closet cutie friend just sticks mainly to Isacord.