I'd skip Excalibur between Cross-Time Caper and Alan Davis' run (#27-42).

I'd skip Wolverine between Claremont's departure and Hama's run (#10-34).

I wouldn't skip any New Mutants, since you're up to Fall of the Mutants already anyhow, Inferno is pretty critical for them and then there's only one storyline between that and things picking up again with Cable.

Uncanny is solid all the way to Mutant Genesis.

X-Factor could arguably be skippable between Inferno and X-Tinction Agenda, but I'd pick it up again with Agenda onwards.

Samy wants to see the following collected editions:
X-MEN: CLAREMONT/JRJR OMNIBUS, X-FORCE OMNIBUS VOL. 2, 
NEW MUTANTS OMNIBUS VOLS. 1-2, GENERATION X OMNIBUS
PUNISHER (1987) #1-18 OHC,
PUNISHER WAR JOURNAL (1988) #1-24 OHC,
X-MEN: REVOLUTION OHC
X-TREME X-MEN VOLS. 1-2 OMNIBUS, WOLVERINE: HAMA/SILVESTRI OMNIBUS,
LEGION ARCHIVES VOL. 14, KNIGHTFALL OMNIBUS
LEGION OF SUPER-HEROES: EYE FOR AN EYE DELUXE HC