I've always ridden with a Camel Bak, so I don't carry bottles, so I use the holes to just carry HEX head screws of different lengths, specifically the type I would need in a quick fix on the trail, although I'm sure you're talking about a roadie bike. I ride strictly off road and you never know what may wiggle loose. I've lost no less than 5 bottles on the trails above Goldbar, WA. over the years, as well as an Avenir Pocket Max pump.

You could also use the screws to hold important replacement parts. 'Ain't pretty, but functional.