to me it wout be naruto and hinata but some crazy people prefer sasuke and naruto pairings. [uuckk]
I believe the most popular Homestuck pairing may be one of the canon ones, although Karkat x Terezi is quite popular.
the reason it's popular is because people (such as myself) beileve that naruto is in love with sakura in shippuden. and she starts to like him =]making them a pairing
Naruto Uzumaki
Seungho and Mir.
The fight Between naruto and pain
I read somewhere that it's NejiHina.
Naruto
NARUTO SAUSKE SAUKRA AKATSIKUI ORG. SAI (atm) KAKASHI TSUNADA GARA
I think it is Naruto or Naruto Shippuden
shikamaru
konohomaru
Naruto seems to be the most popular manga, almost every single site has Naruto as their #1.