TRON/Fridge

Fridge Horror

It was stated in the novelization and hinted in the script that Programs have some vestigial memories and emotional patterns from their Users. Also, the closest we get to an explanation of why the Programs are what they are is Gibbs's line about "our spirit remains in every program we design." Gibbs may have meant it metaphorically, but the in-universe explanation is probably very literal.

The whole Tron/Yori ship: I realize that, in-film, the whole ship was probably just an "as above, so below" shout out to the Bradleys and a means to point out that the Program and User worlds were Not So Different. It was still very sweet, especially in the Daley novelization. A moment fridge brilliance is involved when it hit me - she's a system maintenance utility and he's the damn firewall. Of course they're practically designed for one another.
- Is she? I thought she ran simulations.
  - She does - and therefore has local admin access within the minicomputer that's running the research simulations. in the "outside", and in real life, if ENCOM's running, say, IBM's family of mainframes and minis, then the lab would have most likely been running off a System/34 mini, which would talk onwards to the main kit. Or the Solar Sailer project would have been running on this gear. Lora would have higher-level access locally, hence Flynn was trying to authenticate at a higher level and ride admin privs in. - alcockell
  - She is some kind of debugging or rendering utility for the laser. When Gibbs & Lora are shooting the laser at the orange, there's a readout in the lower right that says "Rom Yori, Load Yori."

The original movie makes more sense if you make it your personal canon that the MCP is oppressing the other programs on the system not by depriving them of energy, but rather CPU time. And the Space Whale Aesop is, don't give an AI program sysadmin privileges over the system it runs on.
After Walt Disney's death, there were (very false) rumors that he was put in cryogenic stasis. The rumors were fueled inadvertently, in part, by Disney staff making comments about proceeding with company decision making, "as if Walt were still here." Now, think about this and the "Flynn Lives" movement...
Whenever a program expresses extreme emotion their Tron Lines light up. The only other time that happens is when Flynn, Ram and Tron are drinking from a Pure Energy Well. Much like us humans who get tired when we let out extreme emotions, the Programs burn more energy doing the same.