More Fog: Permanent (1 Air quantum)
All permanents have a 30% chance of avoiding destruction. The chance is 50% when you have a Fog Shield.
The name could be better, and if the effect is board-wide the check for a fog shield should probably be as well.
Seems a bit strong as it is above, but with lower percentages and/or higher cost it should be OK.
Shrapnel: Permanent (4 Fire quanta)
When a permanent of yours is destroyed, the enemy takes 4-5 damage. Shrapnel itself cannot be destroyed or stolen. This damage stacks.
Should be fine, though I think the wording would be better as:
"When a permanent of yours is destroyed, Shrapnel deals N damage to your opponent. Shrapnel cannot be destroyed or stolen."
N being whatever. I suppose you meant 4 for normal and 5 for upgraded. Correct?
Might be ok without the "of yours" bit even, though the damage should probably be a bit lower in that case.
Jury-rigger is way too complicated, both to implement and to describe on the card.
Giant Honeycomb: Permanent (18 Life quanta)
All permanent destruction attempts are redirected here. GH can survive 6 hits from such sources, and bees rebuild one hit per turn.
High cost as balance can only go so far before you get to the "can't be played or is still too strong" point.
Also, redirection is a bit complicated, at least when combined with other replacement effects.
Bonewallwall: Permanent (4 Death quanta)
When a permanent would be destroyed, sacrifice 2 creatures with no more than 3 in both stats to negate the destruction. If the destruction is successful anyway, you gain 3 Skeletons.
Too complicated. Would require passing control during a turn and multi-targeting, neither of which we have now.
Building Martyr: See Jury-rigger.
Pure Evil Duct Tape: Permanent (7 Darknesse quanta)
All your permanents take 2 hits to destroy, except for Bonewall.
Would require some kind of 'cracked' symbol/status. Might be a bit too strong.
Magnet Drone: 2/3 (2 Gravity quanta)
When a permanent destruction would occur on one of your permanents, you have 2 Gravity quanta drained and a pillar of yours is hit instead.
Simple Wall: Permanent (2 Entropy quanta)
Permanent destruction is redirected here. SW can survive two hits.
Again with the redirection. Overly complicated for not much benefit.
Forcefield: Permanent (4 Time quanta)
Permanent destruction is redirected here. The first hit turns on a 3 meter. A turn passing or another hit reduce the meter by 1, Forcefield is destroyed on 0 meter.
Again with the redirection. Again with the count-down. See Jury-rigger and the others.
Resonance: Permanent (7 Aether quanta)
When a permanent of yours is destroyed by the enemy, a same-type permanent of enemy's is destroyed too. This can hit through all sorts of protection, but you can't destroy your own permanent for this to trigger. Resonance cannot be destroyed of stolen itself.
Alternatively, Resonance can cost 4 and not be protected.
Possibly too strong. Should definitely not be protected. Different wording:
"When your opponent destroys a permanent of yours, a same-type permanent of theirs is destroyed. This can hit through all sorts of protection."
I find it somewhat amussing that you, who are so vehemently opposed to protected critters being affected by anything, are suggesting something that hits through perm-protection...
On all of the above: how does this apply to stealing?