"References" (variable aliases) make your code harder to understand and could be a source of hard to follow errors. There are no valid reasons to use references in php and to be on the safer side try to avoid them altogether.
And no, objects in php5 have nothing to do with "references".
"References" as implemented in php is a strange concept. Normally, in programming languages variables are independent of each other so that changing one variable doesn't affect others. Php "references" allow several variables to share the same value and to be dependent of each other. Basically, you change one variable, and suddenly another one, which you think is totally unrelated, is getting changed too. It's no good thing and often leads to much confusion.
Objects in php (do I need to add 'five'?) have nothing to do with "references" in the above sense. They behave much like C pointers (actually, this is what they are under the hood) - when you pass an object to a function, you actually pass a pointer, and the function can use this pointer to manipulate the object contents, but there's no way for the function to change the passed variable itself, for example, make it point to another object.
This "objects are references" misunderstanding is probably because people confuse php "references" (ampersand syntax) with the generic CS term , which also applies to pointers, handles etc.