I have a Toshiba laptop with Ubuntu 11.10 installed, all works fine. If I connect a wired phone (RJ11) into the RJ11 slot in my laptop and someone calls that phone, is it possible to accept a phone call from within Ubuntu and use the laptop microphone/speakers to communicate?
Since you mentioned RJ11 this likely means you have a standard modem in your computer, this usually means that you need a softphone sometimes called a telephony application that uses the modem to accept and initiate calls using PSTN.
If you can find any such application for Ubuntu that you can install and run properly, what you ask may work, I do not know of any such application I could point you to, and if you are lucky to find anything it will likely be very old.
What is happening nowadays is that VOIP based softphones such as Skype and Ekiga has taken the focus, these phones use packet based methods to communicate meaning that they use your Internet connection to send and receive packets as opposed to a switched network.
When you say all works fine I suppose you mean the modem as well, in short If you do not have a telephony application that uses PSTN running or you modem does not work with Ubuntu then no.
