I understand using a serial interface ie, troi serial plug in... how would one connect to a Linux computer running a voipPBX CTI application?

Any ideas where to start

It all depends on the VoIP system. I doubt that you will need to resort to a serial port; in fact, I'm not sure the serial port could help you with any VoIP system.

VoIP phone servers are just computers which specialize in telephony. As such, they usually include an API for developers to trap for events, such as incoming and outgoing calls. I bid on a project once to integrate with Switchvox (an Asterisk-based solution from Digium) but the high cost prevented the client going forward with it. We were going to write a little FileMaker plug-in to capture these events, write them to a log, and -- if the employee was logged in to the database -- sent an event to the FileMaker client to perform a screen pop so they can log notes in the database.