I think the Mario Party games could probably be disregarded, seeing as Mario Party 6's intro says it takes place in "Mario Party Land." However, if we allow for games to be wherever we want on the timeline (as we already have with Yoshi's Island), then the Party and other spin-off games could be set many years after the main games. For example, maybe after Bowser stole the Music Keys in DDR:MM, no one took him seriously anymore, and he no longer had any real power, and was reduced to crashing Mario's parties.
This is also a possible explanation for Baby Mario and Baby Luigi showing up in the spin-off's: After all the main games (including future ones for many years to come) Mario and Luigi married Peach and Daisy, respectively, and had kids.
I don't think the spin-off games necessarily have to be set after the main games they reference, because the places still exist later. (Mario Kart DS proved this by bringing back courses from all the other Mario Karts and having new ones set in SMB 3 and LM. Of course, then we'd have to deal with the fact that the haunted mansion actually disappeared as soon as Luigi left it, leaving absolutely no time to race around it, so it's probably best to approach the spin-off games the same way things are dealt with in the official Star Wars canon: anything that contradicts higher-level material (in this case, the real games) is disregarded, while everything else is canon until higher canon contradicts it.)