I want a flat shading effect in my game, where colours are assigned to each polygon instead of each vertex (I don't want any vertex colour blending). I know that flat shading is available, but the polygon colours can only be controlled by setting the colour for the right vertex in a polygon (either the first or last one; I don't remember). Since I'm loading/converting my models from files like OBJ, I'm not sure how much control over the final ordering of the vertices in each polygon I have. Also, I intend to use vertex arrays (probably switch to vertex buffer objects later) and as far as I can tell the colour arrays specify the colours for each vertex only. I'm also planning on using some basic shaders instead of OpenGL's built-in lighting and colouring model. Would this effect anything?

unless u use immediate mode
u will need to duplicate the vertices, ie have multiple vertex positions in the same place but each having a different normal

Well, in that case I guess I'll have duplicate vertices; each triangle has their own vertices, and each vertex of a triangle has the same normal.

The thing is that I'm going for a retro look, sort of like Darwinia, which is why I'm trying so hard to get the flat shading "right."

Though I guess I'll ask: say my models have 50 to 200 triangles. With the vertex duplication thing, I'll have to store 150 to 600 vertices. Would vertex arrays/VBOs still be faster than immediate mode (which wouldn't have duplicate vertices, and would let me keep a normal for each triangle instead of each vertex)?

yes most likely faster.

dont be afraid of duplicating vertices, most games even back in the quake2 days do it.
eg a quake2 model might have actual 300vertices but have 800 unique ones in the file,
its not just cause of normals but any data eg texture coordinates