I recently bought a Trek Checkpoint SL 5 and it is billed as a gravel bike but it's also designed for bikepacking, which means it has threaded holes all over the fork and frame. Trek plugged those holes with little rubber plugs which don't have great retention; I've already lost several.

While some people plug the holes with M5 screws, I wanted something that was a replacement for/improvement on the rubber plugs. I found rubber plugs on Amazon that seem to fit just great. The only holes they're not good on, are the ones on the underside of the top tub (the ones for the frame bag). I think those are a different style of insert and the threads start a little deeper in the hole so the plugs don't quite engage.

Anyway, these are less than $6 for 25 plugs and they seem to stick in more securely than the ones that came on the bike.
Link to the plugs on Amazon: https://www.amazon.com/gp/product/B0...0?ie=UTF8&th=1
If the link doesn't work, try searching "uxcell 25Pcs Silicone Plugs, Rubber Round Snap in Locking Hole Plugs for 4.5mm Hole, Hole Stoppers Waterproof Hole Plug for Metal Tube, Furniture End Caps Inserts, Black"