http://www.gamesas.com/index.php?/topic/1083965-soul-gems-what-are-they/page__view__findpost__p__15794817 reminded me about what I've read regarding enchanting items in TESII: Daggerfall. The process is inherently dangerous; if your weapon or armor breaks, there is a chance that the soul used in the gem to enchant your weapon is released and attacks you; your weapon would lose its enchantment.
Another possibility is to increase the danger by adding any souls from soulgems used to recharge an item. So, if you initially used a frost atronach to enchant your item, then if it breaks, a frost atronach will spawn and attack you. If you recharged your item with a rat, then if your item breaks, both the rat and frost atronach might spawn to attack you.
And by "breaks" I mean totally broken, 0/2000, etc.
There could be % chance of the souls escaping, possibly depending on your enchant skill (if such a skill is brought back for Skyrim). The higher the skill, the lower the chance that when the item breaks, the soul(s) will escape and attack.
Secondly
I think I'd like to see the feature that if you apply a negative enchantment effect, you should have more "room" to put in a bigger positive enchantment. For example:
I have a pair of boots with a capacity of 50 enchantment points.
I can put on a positive enchantment effect of Fortify Speed 20pts for 30secs on Self. That takes up all 50 points.
~OR~
I can put on a negative enchantment of Drain Magicka 10pts for 15seconds on Self. This is 25 points. But, because it is a non-beneficial effect, it ADDS 25 points. So, I effectively would have 75 points.
Then, I can put on Fortify Speed for 30pts for 45secs on self, which costs 75 points.
The TESIV and TESIII enchantment systems would be like:
okay, so you added the negative enchantment that costs 25 points. Now you only have 25 points left for your positive enchantment.
Spellmaking could use this advantages/disadvantages system, too!