So many choices and just so many feuds for John Cena. As much as I may not like him as a performer, I have to admit he's had some memorable feuds, but now that I think about it, those feuds were largely the result of who he was feuding with, not his own ability.
I started watching WWE about 5 months before Cena/Edge, so that feud just really sticks out to me. I still vividly remember Edge throwing Cena's title belt into the Long Island Sound, only to have Cena throw Edge in later in the show. Oh TV-14...
I also own Cena/Taker, Cena/JBL, and Cena/Carlito and Jesus on DVD and those were all intense feuds. The Taker feud got him noticed, the Carlito and Jesus feud sent him to the main event, and the Cena/JBL feud got him the title.
Overall I have to go with Cena/Edge because it's the most memorable for me and it just went through so much and so much happened that it makes it the best Cena feud of all time.