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The creator of the Emergency Medical Hologram - EMH (beginning with Mark I), Dr. Lewis Zimmerman, was the 'Director of Holographic Imaging and Programming' at Jupiter Station. It can be expected his work included holodeck technology.
Are there any references in canon, or EU, that tie the technologies together? Ie, the holodeck: 'Molecule-sized magnetic bubbles replace molecules in full resolution holographic objects, which a computer can manipulate individually in three dimensions'.
It is not specifically stated that the Doctor's technology is identical to holodeck technology.
That said, there's ample evidence to support it - the holoprojectors in Voyager's medbay have been damaged multiple times, and replaced from spares.
In the episode where the ship is slowly converted into a massive holodeck for war games (The Killing Game, season 4 ep 18 & 19) the Doctor is seen to travel through holographic regions of the ship (outside of the holodeck) freely.
Moreover, prior to getting the Mobile Emitter, the Doctor transfers himself to the holodeck on many occasions. This shows that his program is fully compatible with the holodeck's technology.
Even more to the point, we see in later seasons that there are extensive holographic entities in the Delta quadrant (to the point where some species have laws against harboring them, and they are used by others as practical slave labor).
A group of renegade holograms (influenced by Star Fleet's basic holodeck technology, from which many were first created) kidnap the Doctor in Season 7's Flesh & Blood (season 7, episodes 9 & 10). They create a place where holograms can live free, and the Doctor has no trouble transferring his program to their emitters.
In short, there seems to be a standard photonic technology in the Star Trek universe that all cultures use a version of - this is most likely driven by some fundamental law of physics within that universe. All holographic technologies are essentially compatible, individual programs, however, will have varying levels of complexity (with the Doctor being very complex).
