I just got EF a couple of days ago and just finish it. I downloaded some mods from www.effiles.com and follow the instruction here: http://www.effiles.com/file.stuff?body=LoadingCustomMaps I go to the In Game Menu/Mod and I only see the Single Play and the Holomatch mods. I did patch to v1.2. My system is fully patch.
MS XP Pro Athlon TB 900mhz Geforce 2 MX 386 Megs Ram
Not every mod will show up on the MODS function. Most PK3 files (unless stated) will go into the BASEEF folder. However MODS like Colony 7 don't go in the BASEEF but in the Star Trek Elite force folder. MODS like Colony 7 usually come with a .bat file that you can click on. MODS like Hazsucks which alter the character's appearance (eg uniforms) automatically change the character's appearance without selecting anything.
Hope this helps..