Here's some information on the major differences between Dark Dungeons and the Rules Cyclopedia, in the author's own words.
There are very few changes that are deliberate "house rules" as opposed to merely having to try to come up with something that reconciles contradictory rules in the original RC (of which there were a surprising number once I went through it with a finetooth comb...)
* I'm treating various optional rules (weapon mastery, high level demi-humans, skills, Immortals, etc.) as core.
* I've reduced the amount of XP needed for high level demi-humans.
* I've given demi-humans weapon mastery that works like everyone else's rather than the "all weapons at first level".
* My skill list is different from the RC's skill list, to avoid overlap with class-based abilities.
* I've changed the way magic-users and elves learn spells to make it consistent with the way weapon mastery is learnt.
* I use a "statement of intent" at the beginning of a combat round (this was apparently supposed to be in the BECMI rules but was accidentally skipped - although some spell descriptions assume it's there).
* I treat the "confidence level" of a dominion as an ongoing score that can go up and down, rather than a score that's calculated freshly each year.
That's the main changes, I think. There are lots of little fiddly bits where rules (particularly optional rules) conflicted and I had to make a "house interpretation" of the rules - but the ones listed above are the main deliberate changes.
This is taken from the Dark Dungeons: Rules Cyclopedia is back! thread on RPGNet.