I've been messing around with this as well, and there are a few good options now, if you're willing to self-host services:

- calibre-web, as a pure web front end to the calibre db

- Calibre Web Automated, which is a rewrite of the app, with a better web UI, that is faster and adds functionality

- Grimmory, a Java-based book mgmt. app w/ a web front end too

- BookOrbit, similar to Grimmory but written in Node and seems to scale better w/ 100k+ book libraries

The better way to get books onto KOReader is via connecting to these apps' OPDS feeds. Wireless, and most of these other apps have better library organization.