Empty cells can be crafted using Tin from electrodynamics (or any other modpack where Tin ore is supported) and glass. Empty and some Fuel-containing cells are stackable (64). Most fuels are radioactive, so wear a Hazmat Suit.
Fission Reactor Fuels
Fission Reactor can be powered using low and high enriched UO2 rods, as well as plutonium fuel rods. Those can be crafted using empty glass cells and Uranium-235/238 and Plutonium-239, which can be obtained from Gas Centrifuge and Fuel Reprocessor respectively.
However, generating heat is not the only functionality of the Fission Reactor; it can also convert Deuterium cells to Tritium cells. Both are required to power fusion reactor, while Deuterium can be obtained from enriching heavy water cells in chemical extractor.
Currently, there are only two fuels available for MSR: LiF-ThF4-UF4 and FLiNaK salts. Both are obtained through MSR Fuel Preprocessor machine using Hydrogen Fluoride and their respective reagents. Molten LiF-ThF4-UF4 salt keeps the reactor hot enough, while FLiNaK salt serves as a coolant delivered to MSR via freeze plug underneath.
Fusion Reactor Fuels
As mentioned above, Fusion Reactor fuses Deuterium and Tritium fuel to generate massive amounts of plasma, boiling water around it and powering the steam turbines.
There is currently no way to capture plasma into an empty cell, but perhaps future technologies will allow a way.
Darkmatter cells can be obtained via the particle accelerator, specifically through the particle injector block. Check the respective wiki page for how to efficiently set up the accelerator to produce those. Shall your accelerator be too inefficient to give the particle maximum possible velocity, you will end up with antimatter. Large amounts of antimatter can be used in Ballistix mod.
Electromagnetic cells are required to power the particle injector block, consuming any random item and a single electromagnetic cell upon launching the particle into the accelerator. In theory, electromagnetic cells can themselves be used as a particle source.
Spent fuel rods can be scraped for remaining fissile dust using radioactive processor. This dust can in the long run be converted to Plutonium-239, but Hazmat Suit must be worn when carrying spent rods and/or Plutonium-239 intermediates.