A. Plantinga's Hypothesis: all such evils are caused by abuses of creaturely free will - either human or superhuman (fallen angels). Remaining problem: Plantinga must explain why God would make us so vulnerable to these evil choices.
In the case of human wrongdoing, one could argue (as for instance, Lewis does in the Problem of Pain, and Swinburne in pp. 216-221 of The Existence of God) that such mutual vulnerability is what gives human action much of its meaning and significance.
But, what value is there in leaving us asymmetrically vulnerable to the actions of superhuman agents? Perhaps there are values involved here that we simply don't understand.
B. The curse of Genesis 3.
On this view, human beings were originally created so as to be exempt from death, disease, suffering (all pain, or only excessive, pointless pain?). After mankind's fall into sin, the natural environment of humans was changed, introducing non-moral evils. Some problems: (a) Why and how was the sin of the original generation transmitted to later generations? (b) If the curse is a kind of punishment, why isn't it distributed in proportion to guilt (cf. the biblical book of Job)?
C. As integral to human nature. On this view, human beings (like other animals) are naturally subject (at least in this life) to pain, disease, predation, disaster, etc. Human beings couldn't come into existence except in such a world. The distribution of evils is primarily due to chance (cf. van Inwagen's paper).
x One could perhaps form a hybrid of 2 and 3. Human beings are naturally animals, and so subject to natural evils, but naturally endowed with a special dominion over nature that would have exempted them from these evils. At the fall, this special dominion was stripped from mankind (to prevent its abuse), reducing humans to an animal level of existence.
D. What would a world with moral evil but no natural evil look like? Very similar to Aquinas's conception of hell: the pain of hell is the pain of frustration, as wicked men are unable to carry out their evil intentions.
A. Due to superhuman agents, or as a result of the Genesis 3 curse. The second would require some explanation of apparently pre-human fossils.
B. Allowed for the greater good (Swinburne).
Provides humans with knowledge of the consequences of their actions (including similar actions performed upon other human beings). But - couldn't God have provided this knowledge innately?
C. Provides opportunities for the performance of morally good actions - compassion, patience,...
D. As integral to the nature of the animals. Austin Farrer's "Physical Accident" chapter.
In Farrer's earlier book (The Finite and the Infinite) he argued that creation necessarily involves a "splintering of being". God created a true multitude, not a single, smoothly functioning Cosmic Machine. For such a multitude to exist, there must be a "chaos of conflicting forms", that is, each created "substance" (independent being, like an organism or a particle) must have its own drives and propensities, uncoordinated and uncorrelated with those of distinct beings.