(A collection of tidbits that caused me to stare at my screen wondering WTF?? for a ridiculous amount of time.  I'll be adding to this as appropriate)

1. [2007] If you update the permissions on a folder (deleting RoleAssignments) AFTER setting the unique permissions on an item IN the folder, the item-level permissions are wiped out - even though the item is set to NOT INHERIT permissions from its parent.  I think the same holds true for Webs and Lists.

2. If you're building a custom app on SharePoint, never, ever, EVER use the default Title field in a custom list/content type.  It carries FAR too much baggage.

3. When working with the ASP.Net Navigation provider, somewhere it uses the URL of a Node as the Key in a collection so if two nodes have the same URL, only the second node will be in the collection.  I typically trip over this when putting in test nodes.