The only things worth transporting will be things that can not be replicated easily. With stated replication technology biological compounds will be nearly worthless. Spices? Every Omni-maker 333 will make every known and unknown spice. Silk? Socks are made of this stuff. Drugs (in both meanings)? Just input the name, you may have to void the warranty on your device, though (we will get back to artificial scarcity later). Steel? Supply enough iron. Spaceships? Just add blueprint.
Manufactured goods will not be worth transporting. There will be few types of goods worth transporting, but the only tangible ones will be:
Rare elements
Hydrogen is the most common element in the universe. Helium is abundant. Oxygen and carbon are dime a comet. But Osmium? Rhodium? Iridium? That stuff is rare on earth. Estimated 2012 US production of Osmium was 75 kg, world production isn't known at all, but most likely is below 1000 kg a year. And we are lucky to have it at all. If not for the fact that Solar system was formed out of a nebula left behind by dead supernova, we wouldn't have heavy elements at all; thermonuclear synthesis stops at Iron, synthesizing heavier elements is endothermic, not exothermic and thus elements heavier than iron are created in very final stages of life of heavy stars. When heavy star dies, it disperses those elements, along with usual bountiful of light elements.
$6*10^{23}$ atoms of Osmium would weight 76 grams. Industrial production of heavy elements is impossible and is unlikely to be feasible in both near and not-very-near future. Perhaps one day, in a thousand or more years, but not any time soon. Until then, elements like that will remain valuable, especially if they are found to have further industrial applications driving demand. Nebulae left behind by Superheavy supernovae will be sifted for rare elements, any planets which somehow survive supernovae will be mined, systems which contain higher concentrations of heavy elements will be important mining and trading hubs.
Information
FTL engines don't imply FTL communications. Without FTL communication, messages will be carried by courier ships. This will include everything from personal messages (letters), through zines (limited communication would lead to rebirth of newspapers and magazines), databases, entertainment (films/games/music/etc) to intel procured by industrial and military espionage.
Even if your world has FTL communications, it still doesn't mean courier ships are out of question: all widely used encryption methods are breakable, they just rely on breaking them taking impractically long time. Quantum computers are said to nearly instantly invalidate all of present encryption. If your world has quantum computers, no communication is secure, and you need courier ships to carry single-use keys. There is only one encryption method which is proven to be truly unbreakable: random single-use keys longer than message itself. Keys can not be procedurally generated, they have to be truly random. Quantum encryption is just a fancy name for dynamic generation of single-use symmetric key between devices within line of sight (optical fiber-enchanced line of sight) of each other, it won't work between star systems, it might not even work between planets in same system.
Therefore, world with FTL communications and quantum computers will have courier ships carrying secure hard drives full of single-use keys, paired with predefined receivers in other systems. Depending on world details, it might be huge corporations akin to present day ISPs supplying keys to subscribers, or it may end up with smaller-scale key-merchants, flying around, creating paired keys with receivers in every system and selling those keys to whomever wants to buy, or both.
Antiques and art
In presented technology, it's possible to perfectly replicate physical properties of any and every work of art. But for true snob that won't do. He will want real antique, certified, with long data trail at every possible place proving that his item is genuine. Objects like that will be worth transporting, because some nutty snobbish collector will pay enough to make it worthwhile.
However, it's important to remember that quality which makes them worth transporting is completely intangible. Perfect replica will be indistinguishable to the molecular level. There will be no differences apart from perceived "continuity".
This artificial scarcity, leads us to last possible trade good:
Law-enforced artificial scarcity
What stops you from copying a game? In world with perfect replication, physical objects will be as easily replicable as cracked game over internet. Thus, it's absolutely certain that industrial lobbies will stand on their proverbial ears to get governments to pass laws disallowing replication (laws like that are in effect today, with personal replicators, those laws would only get stricter), and replicator manufacturers to program replicators to somehow prevent copying. Heck replicator manufacturers will likely want to prevent copying of their own machines. Perhaps replicators will be programmed to look for steganographic watermarks, or specific molecular patterns, and disable replication in case those are found, maybe physical cartridges with encrypted chips will be required to authorize fabrication of restricted goods (a bit like present printer cartridges with chips preventing refilling) perhaps some other way will be found. Either way, internet-equivalent (either FTL-internet, underground zine network or something else entirely) will be full of bootleg designs and tutorials how to bypass copy protection on makers (which will void the warranty).