BitStamp has always worked great for me. The only issue I experienced was my fault (although their support would not get my full marks). I can't say the same of MtGox for sure.

In regards to the missing transfers problem, here my conspiration theory based only on posts in this forum:

* there has been a software fuckup starting 12.11.2013 and ending 15.11.2013.
* they communicated about it first on 18.11.2013 and then on 20.11.2013 said it's all resolved.
* it's not resolved for some and support has gone unresponsive on them: some transfers on 12.11.2013 seem to have ended up a black hole.

Now fixing this one is a delicate matter and depends on why and how the data is missing (hardware fuckup? insider theft? bank stole the money? do lawyers need to be involved?). Every cent needs to be accounted for. Some people are surely trying to scam BitStamp by claiming they sent money they never sent.
Also they need to be careful about their communication because admitting the fuckup might be damaging for their business. And so would be hiding their heads in the sand and hoping it all goes away.

Once more BitStamp has always worked great for me and I hope they do the right thing and restore everyone's faith quickly.