Different ships will use different fuels
Much like today's rockets, the principle consideration will be cost. You have to weigh the potential of a fuel against its mass, thrust, cost, and mission parameters. But since all fuels have the same thrust per mass using your matter->energy converter, then you only have a 3-factor problem. And since in space, drag is so negligible, volume is only a minimal concern which further reduces most missions down to just 2 important factors: Mass and Cost. In other words, you want the cheapest possible material per mass that you can fill a fuel tank with as long as the density is not super low.
Rather than delving straight into costs of stuff here on Earth, lets start by discussing what will make one form of matter cheaper than another. The big thing is of course how available it is. Whatever you can scoop up from next to your space port and load straight onto the ship in bulk will always be cheaper than stuff that needs refining or transportation. Renewability is also a key factor. If you have to keep digging deeper or farther to get something, then it is more scarce than a resource that just keeps coming to you.
The second factor of course will be how easy it is to get onto the ship. Gases are always a bad choice because so much work will need to go into compressing it down into a storable substance, and then you need to transport it under high pressures which has safety concern. So, while it is self-renewing because air will always flow in to take the old air's place, it has a high refinement and storage cost. Solids are generally going to be much more dense and safer in transit, but they come with an even higher refinement cost to break apart enough to move around, and perhaps more effort to grind into dust if it has to be fed through any sort of fuel injection type of system. Solids are also not self renewing: once you take a solid from your environment, no new matter will flow in to take its place. This means that liquids will, almost without exception, be the cheapest fuel source to put onto a ship. They are fairly dense, they flow to replace used up sources, and don't need any refinement before you can pump them into a holding tank. So, any liquid that is also common will generally be the preferred fuel on any given world.
Here on Earth we have oceans of a particularly plentiful liquid called water... salt water, lake water, does not matter for your engine too much since its all just fuel anyway. To get an idea of just how cheap water is, the average cost of 100% unpurified irrigation water to a farmer is about 880,000 tons of water per dollar... now this assumes horizontal or down-hill transportation, but so what? If you build a space port at the foot of a dam, you have no need to even pump the water. Just attach a hose to the fuel tank, open a valve, and let gravity do the filling for you. Beyond the initial cost of the damn and filling station, this makes your fuel practically free and infinite.
.. well not truly infinite, but with ~1.5 quintillion tons of water here on Earth too pull from, it would take a LOT of ships have any noticeable effect on the planet's total water reserves. Since matter has about 9e16 J of potential energy per kg. This means the Earth's total water fuel reserves would be about 1.4e38 J. This is about the total power output of the sun over the next 4.4 million years.
So if water is such a good solution, then why will different ships use different fuels? Simply put, not everywhere in space has liquid water. Go to Titan and all the easily accessible water is frozen solid, but instead you get vast lakes made of liquid methane which would provide a way cheaper fuel source. Or if your space port is on a planet where there is more carbon than oxygen, you will likely see vast oceans of liquid asphalt instead. Or if you are on a more Venus like world, you have the chance of a form of liquid carbon dioxide. If you find an especially young world you might find large exposed oceans of lava: which admittedly might be a bit harder to collect than water, but if you're on a such a world, it's probably still a much easier substance to harness than liquid water.