Since every wiki engine has slightly different text formatting rules, and since most engines allow customizing the rules, the text formatting rules are essentially different for every wiki.
This causes problems in the following areas:
Contribution: Before being able to post, you have to double check the rules. This is hard on newbies, and prevents a general wiki client aware of the text formatting rules.
Copying: You cannot just copy raw text from one wiki to another, since the text formatting rules will be different.
Transclusion: You cannot just include raw text from one wiki to another, since the text formatting rules will be different.
Interwiki Links: To facilitate linking to other sites and wikis, interwiki links act as URL abbreviations. Since these can be defined locally for every wiki, they are also not movable to a new wiki without some consideration.
Copying Local Links: When you copy a raw text from one wiki to another, local links will point to local pages on the new wiki instead of pages on the original wiki. Interwiki links can make this easier, but they usually look ugly. Tiny Wiki has a mechanism whereby you can put a block of text into the context of another wiki, so that all local links will point to pages on the other wiki. This technological solution is neat, but confusing for newbies, since not everything that looks like a local link is a local link. This could be fixed with some CSS.
This is a good example of the problem we're facing in the wiki world.
(Can somebody link to a similar problem description for the weblog world?)