Part 3: post volume 1 - volume 3.
Wolverine #83 - 84 - Heather, Mac, and Logan fight, well, let's face it, a werewolf
Wolverine #91 - 92 - Mac is little more than a cameo in 91, but in 92 he and Heather conduct a medical exam of Logan
X-Factor #112-123 - Wild Child is part of X-Factor; the whole team comes to discuss it with him in 116
Wolverine #95 - the Hudsons help Logan fight something
Over The Edge #2 - Michael fights a snow creature with the power of The Mullet! - he's on about three pages, but it's his own fight
Marvel Fanfare v2 #2 - Heather's around when Logan and Hulk fight Wendigo. Again.
Domino #1 - Puck has an extended cameo discussing things with Domino (followed up in a minor appearance in #3).
Sabretooth: Back To Nature - Wildchild talks to Sabretooth before the latter goes off for a fight
Generation X #19 - Walt appears (but doesn't fight) in a story written by sometimes Alpha scribe Scott Lobdell. This is designed to make Alpha look like a bunch of incompetent idiots. Thanks for that
Wolverine #110 - Michael helps Logan defend a family whose parents look exactly like the Hudsons
X-Men Unlimited v2 #12 - story 2 is an extended talk scene between Logan and a very drunk Judd
X-Factor #124-138 - Wildchild is still part of the team
X-Man #27 - 28 - JM gets kidnapped, so Nathan tries to save her
Deadpool #1 - Deadpool fights Walt in the frozen South
Alpha Flight v2 #1-2
Maverick #3 - dunno
Alpha Flight v2 #3-8
Alpha Flight v2 #9 / Uncanny X-Men #355 - the same story, told from the X-Men's pov and the Canadians'; the Canadians try to get Logan back
X-Factor #141-143 - in the last of these, JM begins to recover from the kidnapping and manipulation (see X-Man 27-28, above)
Alpha Flight v2 #10-16
Alpha Flight v2 ann '98
Alpha Flight v2 #17-20 - Alpha Flight appear in the final two issues to fight the gubmint team
Wolverine #142 - 143 - Wolverine and Alpha Flight fight AIM; Snowbird gets brought back from the dead, presumably as a clone since Walt's currently using her body (not like that!); but they say this is her original body
Generation X #58 - the team fight a sasquatch; then Alpha Flight comes to take it home
Uncanny X-Men #359 & 365 - dunno. Something about Michael
Thunderbolts #43 - dunno
Uncanny X-Men #392, X-Men #112, Uncanny X-Men #393, X-Men #113 - Eve of Destruction, where Northstar joins the X-Men; Barry McGuire does not make an appearance
Black Panther #2 #42 - 44 - Alpha make an appearance in 44; I can't see them by flipping through the rest
Citizen V and the V Patrol #2 - I don't have this one
Wolverine #171 - 174 - Wolvie fights Wendy. Quietly. Then AF appear on the last page; in 172 they all fight Wendy. Mickey and (briefly) the Hudsons discuss it all in 173; 174 isn't an appearance, exactly, but Wolvie wears Mac's costume the whole time
Wolverine #179 - 181 - the team and Logan fight a big fat ugly guy; Pathfinder is intro'd. In 180, Wolvie helps Pathfinder to be trained; 181 is not to hand right now.
Deadpool III #57, 60-61 - dunno
Weapon X#1/2 - members get recruited to Weapon X
Weapon X: Sauron + WC + Agent Zero- members get recruited to Weapon X
Weapon X II#1-13 - contain Jeffries, Wildchild, and JM
Uncanny X-Men #414-421 - In 414, JP is recruited as a teacher by Charlie X, has a character moment involving a mutant kid
X-Men Unlimited #45 - this is an Alpha Flight issue, and shouldn't be called X-Men. Ends in Claire's birth, though she won't be named 'til v4.
Uncanny X-Men #422 - 434 - in 422, AF fight the X-Men so they can take a kid back to Canada. In 432-434, they show up in anti-Juggernaut armour for pretty much the same reason.
New Mutants 2 #2-7 - Northstar's around.
Weapon X #18 - dunno
Wolverine III #25-26
New X-Men: Academy X#13
Nick Fury's Howling Commandos #2 - Sasquatch is on the team; or a sasquatch. Nobody's sure.
Alpha Flight #3 #1 - 12