In iTune's "Capacity" bar, I've pretty much always had equal parts orange "Other", which I assume is Cydia + 3rd party apps, and green "Apps".

After deleting a cracked game app, then syncing my phone, the orange "other" is now missing, and green "Apps" is twice as big.

There was no iTunes update, but it appears iTunes is now recognizing Cydia apps as "Apps".

See the screenshot.