I prefer complete when possible but I will make exceptions.
For GBA games that I simply cannot find complete at a reasonable price (Castlevania: Harmony of Dissonance, Parasite Eve II), I will buy used cart only if I have to (which I did).
For RPG's, I seldom buy unless complete. Part of this is because I enjoy having the original booklets and cover art. Also, in the unlikely event that I would sell or trade my RPG's, having them complete is better for the value. The only one I ever recall trading though is Vay for Sega CD (I am still kicking myself for that one.)
Thanks to EB's policy on including all manuals and packaging with PS2, Xbox, and GCN games, I never buy those unless complete (and that is why I never buy used from Gamestop online).
I am more forgiving on older systems like the SNES, NES, and Genesis.