I've thought a lot about this. Probably too much.
From DG: Consolidated skill list; entire sanity system including bonds, adaptation, and breaking point; and lethality. Character creation by profession packages.
From CoC: The combat system other than autofire volleys being replaced by lethality. The damage and death system. Luck and pushed rolls. Bonus/Penalty dice. Success thresholds. Percentile characteristics.
A comment to a Kickstarter Update got me thinking - When dealing with Mythos Tomes, are there any specific ones that are evocative of a certain theme? How do you impart that tome's "flavor" to your players? For an example of what I'm wondering, I'll refer you to Shimmin Beg's blog posts about "fun-sizing the Great Old Ones" which kinda talk about how to infuse a GOO into a scenario beyond just having it make an appearance (and he's tackling world-ending ones at that). Based on his post, here's a few things to start off thinking with:
cues that can be used to evoke the feel of what the tome is/does
slanting descriptions towards the tome's theme/purpose
NPC behaviors and actions
non-plot events/"random occurrences"
The readers of the tome, whether cultists or not - is their mood or behavior impacted by it, either due to proximity or what they read?
What mythos entities would be logical inclusions for scenarios with said tome(s), that don't just end the game?
You also might want to seek out the material Ken Hite wrote for Pelgrane as part of his Ken Writes About Stuff column. There are three packs available. They have things like new approaches to Cthulhoid monstrosities as well as extra rules named Zooms which look at certain aspects of the rules in depth. The ones on various magic types (Goetia, Voodoo and Alchemy) are very useful. I particularly like the Foul Congeries series as well.