We have played with the Miskatonic university organisation for our last 4 or 5 games and have found it has no effect on game play at all. Where we have managed to get the tokens to activate it we have always found it too late in the game or in need of them for other things. Has anyone else found this to be much use?

Well, I find that the main utility is the Advanced Classes ability, which is (at least at first) generally a better deal than the Science Building's ability. Even if you don't plan on visiting the Science Building in future, it effectively gives you a "bonus" encounter at Administration, which generally has pretty decent encounters (not to mention a very nice ability). The Restricted Section is also generally worth it, since, with the exception of Ancient Tome and (arguably) Dusty Manuscripts, Common Tomes are all quite good (getting a Unique Tome with it, on the other hand, is a terrible idea). Expeditions can be useful, but generally, they're just too expensive to warrant it.