Storm and Wolverine - Throughout all their 40+ years in publication, no other 2 X-characters have shared more panel time together or had their relationship fleshed out as much as these 2, not even Scott and Jean or Logan and Kurt.
Storm and Bishop
Bishop and Gambit
Jubilee and Wolverine
Storm and Rogue
Storm and Psylocke
Jubilee and Xavier - I know this isn't a real friendship, but I really liked that issue she took Xavier rollerblading.
Wolverine and beer
Outside the X-Men, I also like Logan and Spider-man's friendship. Kinda reminds me of Red and Eric Foreman.