You can change the actual file, or create a patch as Mezmorelda suggests. Open up FO3edit (you can do this in the GECK as well but this type of editing is much easier in FO3edit) and click the FWE esm/esp files. Then click on the Projectile header.
The first bullet projectile (at least for me), is 556mmBulletProjectile. Once your on the weapon you want to modify, look under Model --> MODL -- > Model Filename, and change the projectile to Projectiles\762mmProjectile.NIF (you can drag and drop from the vanilla entry or just edit, then copy it over). Under Data, go down to Tracer Chance and modify to whatever you like. I believe the default is 1.000000, which fires a tracer 100% of the time. This is too high for my liking, so I've adjusted the weapons that fire bullets individually, depending on the weapon type and firing type....usually between 10-25% for pistol type weapons (0.100000 - 0.250000), and upwards of 50% for the miniguns (0.500000). I left sniper rifles/silenced weapons unaltered, so no tracers there.
This is just personal preference...having some tracers does enable you to better tell where fire is coming from, but I miss the visuals during firefights...and besides, it doesn't make the bullets hurt any less ^_^