The CRM SDK describes the main differences in plug stages here. However, there are some additional differences between the pre-validation and pre-operation stages that are not documented.
The CRM SDK includes some compound operations that affect more than one entity. One example is the QualifyLead message, which can update (or create) the lead, contact, account and opportunity entities. With compound operations, the pre-validation event fires only once, on the original message (QualifyLead in this case) whereas the pre-operation event fires for each operation.
You do not get the pre-validation event for the individual operations. A key consequence of this is that if, for example, you register a plugin on pre-validation of Create for the account entity, it will not fire if an account is created via QualifyLead. However, a plugin on the pre-operation of Create for the account entity will fire if an account is created via QualifyLead.
Activities and Activity Parties
I've posted about this before, however it's worth including it in this context. When you create an activity, there will be an operation for the main activity entity, and separate operations to create activityparty records for any attribute of type partylist (e.g. the sender or recipient). The data for the activityparty appears to be evaluated within the overall validation - i.e. before the pre-operation stage. The key consequence is that any changes made to the Target InputParameter that would affect an activityparty will only be picked up if made in the pre-validation stage for the activity entity.