The
first request was for stories in which Ianto and Jack had to deal with homophobia, or where Ianto found himself having difficulty with his attraction to Jack.
Stories dealing with homophobia
Dr. Harkness and Nurse Jones--Ghana by
blue-fjords. This is the sequel to
Dr. Harkness and Nurse Jones--Kenya.
Conversing in Words, Fists and Grunts by
blue-fjords John Ellis by
fajrdrako Ashes and Dust by Blucougar57
Hate by Yourworstnightmare (Caveat: I haven't actually read this, but it's apparently about Ianto getting kidnapped because of his relationship with Jack. Caveat lector.)
The "Long Weekend" series by
misswinterhill has Ianto dealing with homophobic members of his family. The stories are, in order:
Long Weekend Sticks and Stones (This is the story where the issues begin to come up.)
Something Blue I wasn't sure if this was what you were looking for, but here a couple of stories that discuss issues Ianto has with his attraction to Jack and/or his own sexuality:
Fault by
skellerbvvt. Not homophobia, but Ianto denying to himself that he's in any way gay despite his attraction to Jack.
Both the Best and Worst of Both Worlds by
smallwaldo. Again, not specifically about homophobia, but here Ianto does a lot of thinking about what it means to be bisexual and not fit in anywhere.
The
second request was for stories in which Jack was cheating on Ianto, or where Ianto was otherwise fed up with Jack's flirting and infidelity.
Cheating Jack and Jealous Ianto
First, here are stories where Jack sleeps with someone else:
That Doesn't Bother You, Does It? by
misswinterhill Half the Battle by
ivy03 The Sometimes Effects Of The 21st Century On Views On Fidelity... by
gersteakknife The journal is friends-locked, but you can request access
here. It's worth it.
gersteakknife seems to be good about getting back to people who request access.
The Seven Deadly Sins (as Demonstrated by Jack Harkness) by Amanda
Exorcism by
notevery A Matter of Time by
demotu These are stories where Ianto is jealous, usually with a reason to be:
Waiting by
dvanulya Belonging by
never-more-fics Green-Eyed Monster by
oncomingscone Inescapable by
nyghtpet Mind Reading by
miss-zedem The Missus and the Ex by
hel-bee I Don't Know, Sir by
lovelyladylooks How to Shoot at Someone Who Outdrew You by
misslucyjane Good Wishes to the Corpse by
smallwaldo So Far From Normal by seether79
Because my readership has shifted a bit in the migration to Dreamwidth, I'll mention again that these aren't recommendations, per se, though they are stories that I feel the person asking will probably enjoy. I draw these links from the pool of stories that I've saved, and if a story is on my hard drive it means no more or less than the fact that I probably read it all the way through at least once. Though I'm obviously going to give weight to stories that I've enjoyed, these lists are merely that: lists of stories that fit certain criteria, and that I think are well-written enough to be enjoyed on that basis.