For rank and file S.H.I.E.L.D personnel, I'd use the soldier from Light City: The Assembly. These folks are agents that have been with the organization, are referred to by their names in the comics, and aren't Nick Fury.
Real Name: Various
First Appearance: Organization: Strange Tales #135 (August 1965)
AC 7  HD: 3+1 Attacks: Pistol (1d6, range medium) Move: 12
Anytime an agent is reduced to 0 HP, there is a 1-3 chance on a 1d6 that it is actually a Life Model Decoy.
In addition each agent typically has a few of the following traits/equipment.
- 1-4 chance on 1d6 to hide in shadows/move silently and backstab (+4 to hit surprised foe, X2 damage).
- Rocket Pack - Character gains fly speed equal to double their movement, must roll less than or equal to character level on 1d6 to take off (agent doesn't need to roll this).
- Energy Weapon - 2d6 damage, medium range
- Vibranium Weave armor, -4[+4] (agent's armor is 4)