A few typos and a few things I'd change:

```Java
/**
* Replaces any existing instances of the given item (as defined by {@link Object#equals()}) or appends the item to the end of the list if not found.
* @param item The item to add
* @param replaceAll True to replace all instances of the item, false to only replace the first instance in the list.
*/
```
Booleans generally should be True to..., false to.... to be totally explicit and makes it a bit easier to read - you only have 2 possibilities :P