I keep all of my figures in bags with all of their accessories in the bag and each bag is in a larger box
...back in the G1 era, i acquired several compartmentalised clear sewing and tackle kits, which worked great for keeping my accessories organised and readily-accessible at the time, but eventually my collection grew expansive-enough that everything migrated into larger sterilite containers... ...more recently, i've migrated my accessories into more-modern clear snap-together beading/jewelry-making organisers, which work great because they're modular, expandable, and the interior comparments can be reconfigured to suit different accessory sizes... ...now that my collection spans several hundred (thousand?) figures, i can't envision any other system scaling viably...these systems are pretty cost-effective and easy to find at craft stores like michael's or hobby lobby...
For MP and most 3rd party, I keep everything in their boxes. For CHUG combiners I put each figures hand/foot and weapons in a sandwich ziplock bag and keep the complete set in a freezer bag.
Pretty much all of my Transformers are holding their own accessories. If not....I either toss them into an Optimus Prime Trailer or Metroplex' chest compartment. (I do this very seldomly) As for My Kamen Rider Sh Figuarts, I keep the original boxes and store the extra bits in those. I've also incorperated the boxes into the display
I just keep mine in a plastic box under my bed. I have like an idedic memory for accessories so I don't need to keep track of who holds what.
Incoming thread necro... with pics! Probably like many of you, my collection has been growing and so has my assortment of accessories. I give you, The Energon Cube. I got this at either Michael's or JoAnn, whichever one has the best coupon or discount at the given time. They were discontinuing them so check Amazon. This is the Creative Options Grab N' Go Rack System for organizing arts & crafts Transformers accessories. They make a small and medium, this is the medium. It has a roomy top section and three removable rack cases. The rack cases also have dividers that can be used for organizing beads and sewing notions Tiny Plastic Weapons. If you have a labeler you could also make labels over each section noting which figures the underlying accessories go with. You might be saying to yourself, "Dude, you bought a pink box." Nope, it's Energon! Because this is decent system and the other available colors are "Even Uglier Pink" and "OMGWTF is That? Blue". Happy collecting!
I don't open my TFs at all...Lol. Seriously, I usually devise some way to mount all of the accessories on the figures while on display. I also have one of those old TF collector cases chock full of stuff.
Some stuff is just in a drawer or plastic bag. When possible, I try to repurpose weapons so that if someone doesn't have one, they can pick up a spare. For example, I have my Encore Predacons individual weapons to various 'bots like Prowl and Bluestreak and then gave their guns to some minibots.
I just have the figure hold the accessories. If there's robot mode weapon storage I might use that too.
I have an Ikea Poppin storage box that keeps my accessories and unused reprolables. All of my Fanstoys extras are in a smaller box, within, just to keep things tidy, since there is so much of it.
I use this, minus the pink box. I have 4 of the compartments boxes (tackle boxes) that I use 2 for Transformers and 2 for Marvel Legends. After that, I have a bigger size box the same dimensions but taller for my bigger accessories like Unicrons wings or the ladder for RiD Prime or the Gun for RiD Ultra Magnus anything that won't fit in the other tackle boxes. I have 4 zip lock bags for the instruction manuals. 2 for the bigger ones 2 for the smaller ones.
You know that place where Prime keeps his trailer... seriously though, I like to use big ziplock bags.