In trying to answer this, I've found a few of the old stories I remember as being hard to track down have since been posted to the AO3. In addition to what evilinsanemonkey's already listed:
Eerie Falls by Yarol2075 was the crossover that got me into Gravity Falls
it's color black or tawny (Dash and Marshall hunt a cryptid) and Typical (Dash and Marshall and sex pollen) by silverkat1620 (the latter is on AO3 now too, I saw) were more early M-Dash stories
Like Hotel California by Lipstickcat, which is future Dash/Mars and a crossover with SCP Foundation
The Supernatural/Eerie crossover series by dancinbutterfly on LJ that starts out Marshall/Dean Winchester, but was going in a Marshall/Simon direction before it stopped updating.
no subject
Three Conversations About Dash X was one of the earliest M-Dash stories I remember reading.
Eerie Falls by Yarol2075 was the crossover that got me into Gravity Falls
it's color black or tawny (Dash and Marshall hunt a cryptid) and Typical (Dash and Marshall and sex pollen) by silverkat1620 (the latter is on AO3 now too, I saw) were more early M-Dash stories
Like Hotel California by Lipstickcat, which is future Dash/Mars and a crossover with SCP Foundation
The Supernatural/Eerie crossover series by dancinbutterfly on LJ that starts out Marshall/Dean Winchester, but was going in a Marshall/Simon direction before it stopped updating.