I get asked this question quite a lot by visitors to the MarioSonicGames.com site. In my opinion, the top 5 online games featuring either Mario or Sonic (or both) are as follows:
Super Smash Bros. Brawl Flash
New Super Mario Flash
Super Mario Sunshine 64
Ultimate Flash Sonic
Ultimate Robotnik Duels
However, this is a very subjective list, and I might give a different answer on a different day. Why not visit the MarioSonicGames.com site and check out the more than 150 Mario and Sonic games there to see for yourself which are the best ones.....