Yes, I think most of it could be solved with common sense, or agreement between players, but a few bits are particularly unclear. For instance, in my spreadsheet I assumed that Extra Clips were treated as Equipment because they were bought with EM's and are listed in that section, but in Paul's spreadsheet they are part of the weapon building process and are wrapped up in the weapon. I could easily see both points of view. Likewise, is Stealth a "system" similar to electronic countermeasures (which can be hit), or is it something interlaced into the armor and structure (which can't be hit)? Again, I could see both points of view. A system that is immune to penetration crit's is much more valuable than one that is not, so this is an important baseline distinction to make, I think.
If we say that everything that is NOT individually listed on the crit chart or part of the armor (which is eroded in its own way) is "other equipment" that implies that they can all be crit'ed. On the other hand, things like Turrets have a slot on the Vehicles crit chart but not the mecha crit chart.
Okay, here goes nothing. I'll make a list of the Equipment that I think are NOT susceptible to Penetration Crit's. Pipe up if you think I got something wrong!
Armor
Ceramic-composite Armor
Crystal Reinforce Alloy
Organic Armor
Superior Alloy
Question: do special abilities disappear when the last AP is lost?
Full Movement Systems
Aerial Mod - Full Flight
Anti-gravity Mod
Aquatic Mod
Hovercraft Mod
Hydrofoil Mod
Submersible Mod
Hmm ... okay, maybe it was simpler than I thought!
About the Extra Magazine, it's listed under Weapon Mod's, so I guess they can't be crit'ed.