Well, you see, I'm planning to state exactly why I came to those conlusions later on. First I have to list all that games. Eventually I'll make a list of all the "Worlds" (universes) and the Marios that occupy them. Here's more games.
The Modern Age(2001-present)
2001
Dr. Mario 64 : This one confuzzles me. Doc is the star, but the rest of the cast is made up of characters in WL3. What universe is it in?
Mario Kart Advance : Another one of those speshal crossovers.
Wario Land 4 : I'm pretty sure this is a direct follow-up to WL3, but signs point to it being set in the universe I was planning to place WarioWare in.
Luigi' Mansion : This one is kinda ambiguous. I guess you could say it's in World II, since that's the main series at this point, but it doesn't explain why the Gallery Ghosts are human or whether or not Bowser was truly dead before the events of this game.
Super Smash Bros. Melee : Now this is important. This seems to be the really big crossover that merges all the universes together, and not just the Mario-related ones. Heck, I think some of them may have been destroyed.
2002
Super Mario Sunshine : Next game in the series. Bowser Jr. makes his grand debut.
Mario Party 4 : I think you now what to expect from one of these by now.
2003
Wario World : Another Wario game in the Warioverse which takes place after WL3.
WarioWare Inc. : I believe this one establishes another Warioverse. It's vastly different from any other Wario game.
Mario Golf TT : This one is intriguing as Diddy Kong appears as a playable character. However, since this was released after Melee, it could be said that all of the different DK storylines were merged into one, justifiying his appearance in the Mario verse rather than the DKCverse.
Mario Party 5 : The Star Spirits as well as a bunch of other characters who only appear in certain universes show up here, only it doesn't necessarily have to be a crossover due to the events of Melee.
Mario Kart DD : This may seem like the oddest place to mention this, but perhaps the multiverse still existed after Melee, as evidenced by WarioWare. It just got downsized a little bit. Maybe Brawl will fix that. ;)
Mario & Luigi : I'm having a bit of trouble deciding whether this is in the main universe or in a new universe because of things like the Koopalings. Then again, it could be argued that Melee caused them and Bowser Jr. to be able to coexist. Either that or Cackletta knows some trans-dimentional magic.
2004
Mario Golf AT : Another one of those games set in the "Real World". Or at least an alternate version of it as depicted by Camelot.
Mario vs. DK : Had the events of Melee not happened, I'd have placed this game after DK '94 in it's own universe. But since the Melee incident, DK's origins seem to have been combined. Or maybe not.
Paper Mario : Apparently the PM universe still exists, unless this happened in the main universe.
Mario Pinball Land : This one seems like it happened right after SMS, so I'll go with that.
WarioWare Twisted : A follow-up to the last one. You may notice I'm going by the Japan release dates rather than the USA ones.
Mario Power Tennis : An interesting thing about this is the appearence of "Ware" Wario in Wario's court. This sorta contradicts all the other stuff in here that hints toward there being a multiverse. Maybe WW isn't set in it's own universe after all.
Mario Party 6 : This games talks about some sort of "Mario Party World". Maybe that's the place where these are set.
WarioWare Touched : Next in the WW line-up. I guess the sign in MPT could be counted as not having been there, but tha takes the fun out of it.
Yoshi Topsy-Turvy : This one hints that the TA universe still exists, as it looks like YI but Bowser is an adult. Plus, there's a bunch of characters that don't appear anywhere else.
2005
Mario Party Advance : This game was crap, but it's still the next in the Party line. (Heh, I made a funny.)
Yoshi Touch & Go : This takes place during the events of YI. Nothing sepesil other than the fact that World I and World II may have been merged together after Melee.
DDR Mario Mix : As odd of a genre choice it masy be, it still counts. What I find odd is that Peach and Yoshi are nowhere to be found.
Mario Superstar Baseball : This one points to there not being a merger after Melee. since it makes reference to Wario owning his own company and DK having an ancestor who wore no tie. If there were no merger, this would be considered a crossover. Actually, I have a way to explain thing for every game after Melee in the case of it not merging the worlds. Maybe the worlds that were destroyed were somehow brought back.
Mario Tennis PT : Next in the series of games in Camelot's "Real World".
Super Princess Peach : Easily set in the main series. Almost had the Koopalings in it. Thank the lord they didn't make it or I'd be stuck (unless I used my Melee theory).
Mario Party 7 : This one appears to be centered around alternate versions of places in the Real World. I can't think of a way to explain this...
Mario Kart DS : Another Karting game. Really awesome at that. Happens to contain references to World I stuff, which would cause me to call this a crossover if my idea about Melee was somehow disproved.
Super Mario Strikers : Some would say that the characters don't really act like themeselves in this game. Perhaps we have another new universe on our hands.
Mario Kart Arcade GP : Now this one has to be a crossover. Pac-Man is in it.
Mario & Luigi 2 : Gives us a look at World II Mario's past, probably the only legit varation of it if my Melee theory holds true. If it's not the past, it's another universe where all the characters are younger.
2006
New Super Mario Bros. : Ah, the return to the glory days of World I. BJ is here, so it can be set in World II, or the "New World" that was created after Melee.
Mario Hoops 3-on-3 : Apparantly a Mario-FF crossover, with basketball.
And that's it for games lists. Keep in mind that there's still new games coming out, so I'll have to add them after I play them (Yes, I have played all the games on this list, save for the ones only available in Japan).