I try to always set things in the same place while I'm using them and put them back where they belong when I'm done using them, or at least at the end of the day. I have a mouse pad to the right of my sewing machine to set stuff on -- keeps it from falling off the counter.
The top drawer of my sewing cart has several wet-wipe containers with the tops pried off. I'm talking about the small rectangle flushable wet-wipe containers. (Of course they are washed and sanitized.) One section is for the stuff I use all the time aka cutting nippers and seam rippers and tweezers, and the others for less often used stuff. The containers can be used on a counter too using binder clips or hot glue to hold them together.