Although Ponting owned the WC 2003 final, I don't see how anyone can see that as one of the best ODIs ever. Favourite? Sure. But best? India bowled so poorly, the quality of cricket was distressing.
My top 5.
1) Australia vs. South Africa - World Cup Semi Final 1999
2) India vs. England - Nat West Series Final 2002
3) Australia vs. West Indies - VB Series New Year's Day Match 1996
4) England vs. West Indies - ICC Champions Trophy 2004
5) India vs. Pakistan - 5 Match ODI Series 2004
One that just misses out, and seems to be fairly forgotten, is the ODI between Pakistan and Australia in the 1996/97 VB Series (Then known as the Carlton & United Series).
http://aus.cricinfo.com/db/ARCHIVE/1996-97/OD_TOURNEYS/CUODS/PAK_AUS_CUODS_ODI3_15DEC1996.html
Brilliant match, the making of Saqlain Mustaq. From that moment on I thought he would become the best ODI spinner in the world. Unfortunately I feel he is the biggest underachiever in world cricket.
That whole ODI triangular series was awesome. Australia dominated the WI early, winning the first 2 matches, but Pakistan arrived and beat Australia many times, WI bounced back to beat both Pakistan and Australia, and eventually topped the table. Australia ended up last in their own home series, and Pakistan and WI moved on to the finals, where Pakistan beat WI in the first 2 finals to win the series. Tremendous cricket.
I temporarily moved from Australia from January 2000 - 2002 so I missed the epic VB series between Aus, NZ & SA.