I have little white flags on terrain bases which I use to mark pinned units (use them for various things in other games too, such as suppressions in Price of Glory).
At the moment we use poker chips for suppressions in T&T, which I don't mind doing but it isn't ideal. I'd like something less obtrusive in the long run. Trouble is you need lots of the things for this game, and making counters and stuff is quite a low priority at the moment when compared with painting figures and making terrain.
Still mulling over what method I'll eventually settle on, same as you. Something that looks good but isn't too labour-intensive (casualty figures are out on that score, would just have to paint too many, though I do use them for other things).
Unlike Hammers, I have nothing against tokens or counters in principle, but only if they look attractive and nice in themselves.