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.
Whenever a program is derezzed rather than fall down dead, whats left of them floats upwards presumably to nowhere. After learning about what MCP does to dead programs, this troper thinks that the ones that get killed also get assimilated by him. In other words the heroes are making him stronger by killing the bad programs.
When Flynn repairs the Recognizer, it makes perfect sense, since he wrote Space Paranoids. He probably is the only User who could repair one, at least so quickly, because he is familiar with the code!
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." — Allronix
According to Cindy Morgan , she was told that Yori has some instinctual knowledge of Lora's life, and she even has an inkling she and Flynn used to fool around.
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. — SuddenFrost
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...
The debate between Dillinger and Gibbs about what their processing goals should be (serving the end user versus serving the business's bottom line) is surprisingly prophetic, as this debate eventually fueled the entire evolution of the PC market that was still in its infancy at the time. In Hindsight, the Dillinger/Gibbs relationship even has a Steve Jobs/Steve Wozniak vibe going on.
Acknowledged by Steven Lisberger, who said that in 1982, it was still unknown which medium the computers would gravitate to: the artists or the businessmen.
The religious parallels between "programs-users" and "humans-gods". Not just the parts where Flynn is basically a Christ figure for the computer world, but the whole fact that not only are most programs not entirely sure if users even exist, but the users aren't even aware that they have created these intelligent beings in their computers. Take this setup a step up into the real world (the novelization takes a few more steps in this direction than the film), and you basically have real-world Deism - the reason we don't see God(s) is because they don't even realize we're here, or self-aware!