Having started with the Pokemon franchise, I would have to say the Pokemon series is my favourite. However, a close second would definitely be the Mario series.
The Mario series of course, and I consider the DK series to be a part of the Mario series. Pokemon is probably my second favorite, with several other Nintendo series slightly behind it.
Mine is actually Pokemon because Yellow was my first game, and Pokemon has always been my most played series. I know offhand that I have 450-some hours of playtime on Diamond, and Diamond is one of my lesser-played games.
Mario is most definitely a very close second, especially the older games.