The System Applications Working Group of W3C has published a Working Draft of the Web Telephony API, which can be used to create apps to manage phone calls.
A typical use of the Web Telephony API, according to the announcement of the working draft is the implementation of a 'Dialer' application supporting multiparty calls and multiple telephony services. The Web Telephony API allows applications to manage interaction with telephony call signaling, but does not handle audio channels management.
The API consists of a telephony manager interface that has a number of methods that you could use to carry out actions starting with making and receiving a call. There are options for hiding the caller identity, and for setting a default subscriber identity that will mean the caller doesn’t have to provide an identity when making a call. Calls can be put on hold and resumed, and new call participants can be added to (or removed from) an existing call. If the service being used can handle waiting calls, your app can put callers on hold and resume held calls. Incoming calls can be deflected to be handled by another number.
Your app can send DTMF tones to the telephony network, and dial an emergency call without having a SIM card. Other options can be used to set the sound volume during a call, to mute and unmute the microphone for a call, and to use headphones with calls.
The API makes use of various existing specifications, including the GSM-CALL suite for GSM, the IMS suite for IMS/SIP, and the Jingle specification for XMPP. The same API would work also for SIP and XMPP calls.
It seems that the Telephony API is more or less the same as the FireFox OS Telephony API as introduced as part of Mozilla's WebAPI efforts. The only change seems to be the dropping of the moz prefix. If you are planning on making use of the Telephony API it is worth mentioning that under Firefox OS only certified apps will be allowed to use it and this means that it is effectively restricted to the phone manufacturer. The reason is, of course, security, but it is odd that an open platform like Firefox OS limits what you can do with the hardware you own.