There are only two relationships that I've seen as true friendships. Beast/Iceman from the original run and Wolverine/Nightcrawler. I mean the X-Men in general like each other (sometimes), but close friendships in comics in general are rare, especially in group books with a lot of characters and too little space to deal with the relationships.
Sandy Hausler
Storm - Gambit
X-23 - Gambit
Karma - Gambit
Bishop - Gambit
It's hard for me to listen to someone not in my position. A caterpillar can't relate to what an eagle envisions.
X-23 and Gambit
Nightcrawler and, like, the entire team.
Scott and Logan.
Cyclops was SO DAMN RIGHT, BABY
Pull list: X-23, Mr. & Mrs. X, Extermination, Spider-Gwen: Ghost Spider, Uncanny X-Men
Have been informed that the Black Swans are "only seeking female members, but thank you very much for your time"
Wolverine & Colossus
I like how Colossus seemed to accept Logan for who he is back in the day when everybody else was still wondering why he was even allowed to be on the team.
Nightcrawler - Wolverine
Hellion - Mercury
Jubilee - Professor X
In general friendships where both characters are challenged in their bs but are not given up on.
Gambit/Storm and Gambit/X-23.
Deadpool/Wolverine/Cap were great too.
TOff the top of my head
1. Kitty and Illyana.
One of the things Bendis did right was restoring their friendship, as Kitty had always been accepting of Illyana's side in the past. So her totally disavowing Illyana didn't feel right to me.
2. Wolverine and Nightcrawler (under CC)
Total opposited and yet they understood and appreciated each other
3. Cannonball and Sunspot
They had a nice complementary freindship, especially in the early New Mutants days. It was fun to see Al Ewing writing them as good buddies again.
Lots of others as well, though.