tl;dr: For calls to the TARDIS itself, the TARDIS appears to route them "intelligently", patching them through when they are most needed. For calls using the souped-up cell phones, they appear to happen in "real companion time".

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TARDIS Direct Calls
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As far as we can tell, phone calls into the TARDIS get connected "when they're supposed to be", without any good rules behind it. However, there is a lot of evidence that the TARDIS herself is responsible for this fortuitous timing, and routes calls to the point in The Doctor's timeline when they would be most directly useful.

The reason we know that the TARDIS itself plays a role in routing the calls is from "The Pandorica Opens". When Churchill has found Van Gogh's painting of the TARDIS and tries to call The Doctor to warn him. For whatever reason, The Doctor isn't available, but the call ends up going to Storm Cage, to the phone outside River Song's cell, where this exchange happens:

> Guard: Cell 46. The Doctor? You mean Dr. Song.

>River Song: Give me that! Seriously, just give it to me. I'm entitled to phonecalls. {he gets the phone} Doctor?

>Churchill: No. And neither are you. Where is he?

>River Song: You're phoning the Time Vortex. It doesn't always work. But the TARDIS is smart. She's rerouted the call.

Since the TARDIS exists in some sense "outside" of normal space/time, the most obvious explanation is that she is able to determine, based on the originating space/time coordinates from the call, when it would be most appropriate to connect to the Doctor.

Some examples of very fortuitous call timing seem to bear this out:

* When Marth & Torchwood called The Doctor in "The Stolen Earth", the call connected to the TARDIS at the *exact moment* that he and Donna had lost the trail to Earth.
* When Clara called The Doctor for internet help, she connected to him at a point *after* he had lost Amy Pond and had met two previous Claras.


Companion Universal Roaming
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In addition, The Doctor has hacked up each of his companions [cell phones][1] to allow them to call home from any "time zone". As far as we know, these calls always connect to their destination at some point where the person receiving the call would "expect" to get it. For the most part, they seem to work in "real time" -- whatever time the call would have been made, had the companion stayed on Earth. With Rose's phone I think this was explicit, but the other cases of companions using their superphones seem to bear this out:

* One-time companion Adam called his mother on Rose's phone, from the distant future, and she got the calls in their correct relative order. (She knew he was in the future and he was feeding her information).
* Martha called her mom rather frequently, and the calls seem to reach her mother in chronological order from Martha's perspective.
* Wilfred claims he was keeping track of Donna's whereabouts from her calling him on her phone, implying that he was also getting those calls chronologically from Donna's perspective.

You're correct that this would seem to open up the possibility of a paradox, if Clara were to call Danny after being on the TARDIS for days, then return home minutes after she left. Why this doesn't happen is never explained, though it's possible that the TARDIS also steps in here and prevents it, possibly by refusing to land at a point where a paradox might happen.

  [1]: http://tardis.wikia.com/wiki/Superphone