This is how I do it.  The key for jewels is that they have 3+ properties that are for 
training skills, mana dependent templates, melee dependent templates, targeted templates.  I do not save any high skills (alone) jewels as those properties are usually a crutch for real skill.  Now if you are building a gimp (many many skills), you will be dependent on skill jewels, but they still need to carry other desirable properties. Anything less that this is usually tossed on a vendor or never makes it through my door.
Training Chest:
Used to pseudo increase skills while training. Example: Ninjitsu +15 ring & bracers, Lower Mana Cost 8%, Faster Cast 1, Faster Cast Recovery 3.  Allows you to cast higher levels, save mana and cast faster if that is necessary.  Also, I put 100% poison weapons & a mage wand (-29) in the same chest.  In fact that is down to about 3 weapons: UBWS one-hand, archery, UBWS two-hand I think.  Skill ideas: Magery, Chivary, Necro, Ninja.
Mana Chest:
Pretty straightforward, with emphasis on mana properties and compliments.  Here save: Lower Mana Cost (5-8%), Lower Reagent Cost (15-20%), FC1/FCR2, FC1/FC3, FCR3, Defensive Chance (5-15%), Enhance Potions (EP 15-25%).  SDI is ok (6-12%) but I don't look for it specifically. Again 3+ properties a must.
 Melee Chest:
Melee Chest:
Lower Mana Cost (5-8%), Lower Reagent Cost (15-20%), FC1/FCR2, FC1/FC3, FCR3, Defensive Chance (5-15%), Enhance Potions (EP 15-25%), plus Hit Chance (10-15%), Damage Increase (20-25%). LRC is less important (generally) here, but is a plus.  You are again looking for 3+ properties.
 Targeted Chest:
Targeted Chest:
These should be focused on a very particular template.  An example should be Parry Mage.  A parry mage needs to maintain 80+ dexterity to effectively parry, so here Dexterity plus Mana jewels are a must.  In fact, I would only keep 4 property jewels here.  A tamer may be another example with skills plus Mana properties.
 
Understand tho, this is for the advanced jewel hoarder.  You mentioned a literal 100's of jewels.  I have probably 50 or less jewels in my house, beyond what my characters might have on.  The first step is to repeat after me... " I am a pack rat" lol.   
