You can easily remove FX from some of the adventures. For instance, just take a look at Resident Evil ... they came up with a scientific explanation for zombies. Now mix liberally with an idea or two from X-Files ... instead of magic, the infected creatures have been possessed by a strange (alien?) virus or strange worms that change their behavior.
You could just use the zombie stats (your players will never know the difference - say something like their organs moved around and their "worm mass brain" is in the thing's stomach to explain the crit immunity) or you could stat them up a bit different.
There's a template from "A Problem at Formid" an ALTERNITY adventure that I like to use instead of zombies. This is converted from ALTERNITY so, of course, feel free to modify for your campaign.
This one works best with a virus, which explains all the massive changes. For worms, take the maniac template
Tainted Virus Template
Str +10 Dex +2 Con +10 Int +6* Wis +0 Cha -2 (you can change the Int depending on how long-term the viral threat will be; higher Int for a longer-term threat). These bonuses are pretty high - you might want to lower them if your PCs are low-level.
Natural Armor +7
Improved Grapple as a bonus feat
Breath Weapon (Ex): Once per day the tainted creature can attack with a breath weapon as a standard action. It does 2d8 points of acid damage and has a Reflex save of DC 10 + 1/2 Con + 1/2 HD. The save DC increases by 5 if the opponent has been grappled (and the opponent can't use Evasion to avoid damage).
Defiling worms would have quite different stats
Wis -2, Cha -2
Rage (Ex): Used once per hour as a free action. The usual (+4 Str, +4 Con) for 1d6 rounds with no ill effects afterwards.
+5 bonus to saving throws to resist massive damage
The demonic ichor in D20 Menace Manual is very close to the black oil from X-Files. Just remove the extraneous special attack and replace it with a radiation attack.
