Bruce/Selina, totally. I also liked Bruce/Rachel (TDK) because of how delusional Bruce was about their "relationship." Rachel pretty much treated him like a child ("They're not gonna let us be together") and clearly had no romantic interest in him. Tate used this to get close to Bruce, so I considered it fairly important.
However I felt Bale/Hathaway had great chemistry together, so I voted Bruce/Selina as my favorite couple.
Edit: Batman11 reminded me of Bruce/Martha and