You'll need to select the upgraded effects (media VPs, as they're called) as a mod in the launcher for them to take effect. Simply fire up the launcher, go to the mod tab, click "Select MOD" and pick the "mediavps" folder from the window that pops up.
If for some reason you don't have it, make a folder by that name in your freespace directory and place the .vp files found in
This thread into it, then do as above. Also make sure to go to the "Features" tab in the launcher and enable the options you want from the graphics category - I'd recommend at least turning on specular, glowmapping, envmapping and jpg/tga textures. With all that done, you should be good to go for a much prettier game.
If you think the game is too bright (many do), you can also add "ambient_factor 40" to the custom flags field in the launcher, replacing 40 with a higher number if you find this new setting too dark, and a lower one if it's still too bright. 40 is just what I use, the 'right' setting depends a lot on your screen so it will probably be different for you.