The Eclipse IDE will consume API calls every time you save or refresh a file; and it's not just one API call per action necessarily, authentication/handshakes consume API calls as well, so saving one change to a file can consume two (or, somehow, sometimes, more) API calls.
In the Winter 14 release, the Developer Console consumes a LOT of API Calls, as it polls for logs and updates the whole time it is open. Leaving the Developer console open in the background will slowly eat up API calls, and we've had two instances in our office of someone working with the Developer Console for a few hours and completely finishing off their 5,000 limit in a DE.
In fact, if you note the number of API calls made, open the Developer Console, wait a minute, maybe open, edit and save a file - you can probably note somewhere in the region of 17 - 20 API calls made.
External tools (such as the Eclipse IDE) record a "login" under the User Detail Page - with an application name telling you what program it was logging in, and you can be fairy sure then that this application will be consuming API calls.
You can also set alert messages if you have a live system which is dependant on the API limit not being breached that will send out messages (at an interval you can set) when it passes certain thresholds.