I read this article over on cracked.com, which says that the transporters convert the object/person into energy and then teleport that. As I recall though, it actually took that matter and "dissolved" it, then moved that matter through physical space and "reassembled" it. Can anyone verify this? (It also helps prevent all of the ethical/physical limitations that were proposed in the article.)
I'm going to my source for this, one I've cited here before, the Star Trek: The Next Generation Writers' Technical Manual, Fourth Season Edition. This is one of the Writers' Guides. In other words, it tells the writers what they can and cannot do on screen.
On page 28, under The Transporter - Once and for All:
... The stream of molecules read by the pads is sent to the Pattern Buffer, a large cylindrical tank surrounded by superconducting electromagnetic coils. It is here that the object to be transported is stored momentarily before actual beaming away from the ship (or even within the ship). It is the Pattern Buffer and its associated subsystems that have been improved the most in the last half-century. While the actual molecules of an object are held in a spinning magnetic suspension (eight minutes before degradation), the construction sequence of the object can be read, recorded in computer memory (in some cases), and reproduced. There are limits to the complexity of the object, however, and this is where the potential "miracle" machine still eludes.
The Transporter cannot produce working duplicate copies of living tissue or organ systems.
The reason for this is that routine transport involves handling the incredibly vast amount of information required to "disassemble" and "reassemble" a human being or other life form. To transport something, the system must scan, process, and transmit this pattern information. This is analogous to a television, which serves as a conduit to the vast amount of visual information in a normal television transmission.
And then, from the same section, on page 29:
From the Pattern Buffer, the molecular stream and the coded instructions pass through a number of subsystems before reaching the emitter. These include the Subspace, Doppler, and Heisenberg Compensators. Each works to insure that the matter stream is being transmitted or received is in the correct phase, frequency, and so on. (sic)
So the object or living being is disassembled, molecule by molecule, converted to a stream that is temporarily stored in the pattern buffer, then reassembled at the destination. The stream contains both matter and data used for reassembly.
According to Memory Alpha:
The object was broken down into a stream of subatomic particles, also called the matter stream. The matter stream was briefly stored in a pattern buffer while the system compensates for Doppler shift to the destination.
The matter stream was then transmitted to its destination across a subspace domain.
So it appears the transporter does use the same matter to reassemble the person/thing as it was made of to begin with, though which particle is which is impossible to track (according to modern physics, at least). This actually sheds some light on the transporter-vs-replicator question too.
In one episode (I am unable to recall the episode title), Captain Kirk referred to the Transporter as an energy/ matter scrambler. As has been stated in the show, the pattern of matter atoms is converted to a pattern of energy atoms, transferred to the desired destination, then the process is reversed, the atom energy pattern is returned to its original atom matter pattern, functioning as it originally did.