I run alistofawards.com which is heavy on multi-ref tagging. I've attached a photo of what some of my award pages look like in the editor with multireference fields. At the moment, I have 400+ categories of competitions. Some competitions include all of them, minus one section - like architecture categories. I know you're thinking, just make another multireference field to add those specific ones. But that would make me have a different collection list which complicates/doesn't allow me to filter/display those tags in other pages -- I need them to all be in one collection. Some competitions cross boundaries, and because I can't really reference another collection in a collection page it gets very tricky. So keeping them in one collection has kept me sane.
What I'm curious about is being able to color tags - or easily tag tags (lol I know, meta, and probably not the right direction). Think MAC folders - how you can color a folder or file by right clicking. This is just a thought, I know most users won't run into the issue having to take out some of the tags. It may be helpful in the upcoming E-commerce sites though.
Another suggestion, maybe take the purple out of these tags so i can more easily scan the text in tags for the ones I need. It is a little hard on the eyes with this many. You could just outline the tags in grey maybe?
I want to stick this note to the board, as it may be more helpful when robust e-commerce sites come available too.