The game manuals themselves list the time passage from one game to the next. However, when it comes to intertwining mainstream games and side-stories, no real information is given.
Recalling a discussion from the last forum, Japanese magazines have confirmed that order for the gameboy games, but also given different orders now and then... Marshmallow Man would know for certain, but he left the community; I can only go from memory. What I remember is that one of them, for example, grouped all the gameboy games in the impossibly short time period after Rockman4. With all gameboy games being separated by several months, and Rockman 5 occuring 2 months after 4, I don't think that proposition really works out.
In the list I presented, I took several matters into consideration: release date, references, characters, abilities, etc.. Which in all cases define an earliest position in the timeline, and sometimes their position at the latest too. Many games need to occur before Rockman and Forte; World5 needs to occur before 6 and 7; World 1 and 2 need to occur before Rockboard; World 1 needs to occur before Soccer; and so on.