With the Mario games, some are made just to be made. They follow a pattern of the Princess being captured by Bowser, and Mario is sent off to save her. You also have to consider which would be canon, and which would not. This is really left up to the player to consider, as really none have been considered canon or not since there is no definite timeline since the storylines are so vague and unconnecting. There are also some games that are obviously prequels or sequels to others, and those which can be speculated as such. For example:
Super Mario World 2: Yoshi's Island
(Prequel to all Mario games)
Obvious prequel to all the other games. This one details what happened to Mario and Luigi while they were still babies. In fact, as early as being delivered to their parents by the stork.
Super Mario RPG: Legend of the Seven Stars
(Sequel to Super Mario World)
At the beginning of this game, Bowser is seen in his Clown Copter, which he uses to capture Peach. The only other game that he had used this vehicle at the time was Super Mario World. At the end of that one, we see him defeated, spinning off into the sky while still in the copter. Therefore, it can be assumed that sometime shortly after he was defeated in SMW, he found Peach again and recaptured her.
Super Mario Bros. 2 (Japanese)
(Sequel to SM
This game, released in America and Europe as "The Lost Levels", was the true sequel to SMB. However, both followed the same exact storyline. SMB2(J) was simply harder levels.
Super Mario Bros 2 (US, PAL)
(Sequel to SM
This game was altered from its original version (Doki Doki Panic in Japan) to add mario characters and storylines, while keeping the same gameplay and enemies/bosses. The reason they done this was because they felt that the original SMB2(J) was perhaps too hard for American or European players, and the difficulty might turn them away from the series. Anyway, it is quite obviously a sequel to SMB, but all the game consists of is a dream that Mario is having. So since the title suggest it sequels SMB, one could place it after that game and/or the Japanese SMB2, some night while Mario is asleep.
That's about all the games I will get into. I haven't played most of the other RPG titles, and when it comes to all the Kart, Soccer, Party, etc., games, those could go anywhere. The fact is, Mario is a universally used character, like Sonic is to Sega. But Sonic had somewhat of a timeline in the game's release order. Bottom line: A timeline isn't that important to the Mario series, and other than the obvious "2's and 3's" associated with the titles, as well as obvious prequels such as Yoshi's Island, they can fall about anywhere. I would suggest listing only the main titles in some sort of timeline, while roughly following their release order as a means of placing them.
Yoshi's Island--SMB/SMB2(J)--SMB2(US,PAL)--SMB3--SMW--SM:RPG--SM64, etc.