It could also depend on whether or not Aranofsky uses any comic material in the script.

The first Omnibus had most of the classic stuff.

Some things that could be added:
X-Men 205 (great BWS art)
X-Men 251-252
X-Men 268 (with Cap/Black Widow)
Wolverine:  Killing (great Kent Williams art)
Wolverine:  Inner Fury (Sienkiewicz)
Hama/Silvestri's run from the first ongoing
BKV/Risso's Logan mini (and maybe some of the other recent 1-shots like Saudade)
I agree Jungle Adventure would be a good choice.

Or Marvel could go for the modern popular sellers and include Origins (the first mini) and Enemy of the State (even though they have their own HCs).