The dark side of the game - AccountantTech - is calling, and I welcome you into its fold! Back in the day I tracked ammo reloads, armor sheeting, actuators, sensor suites, and even ejection seats for my unit. It made running the unit much more interesting and fun to me, as without it, winning and losing just didn't have a real impact. These days I don't track it in such detail for my stories, as I tend to go with whatever makes the story interesting.
I just keep a spreadsheet with the unit inventory in it, and add and subtract from that as needed. MekHQ has a lot going for it, but I find I want to keep more detail than it allows about the inventory, as well as the damage sustained in battle. I like the idea of the warchest system and find it great for a strictly tactical game with no storyline behind it. Unfortunately, I just can't do that - I get too tied into the story and fluff, and can't go that abstract. Knowing I have 25 tons/points/etc of stuff isn't enough, I want to know I have 3 tons of Armstrong AC5, and another 2 tons of Pontiac AC5, and that I have 3 spare medium lasers, but none fit in my Centurion.