Panic, panic, panic. I have been a user on btc-e since 2012, and so far they always came through.  I am not advocating for them, but c'mon this happend before that they are offline for maintenance. They already announced that there is something going on since they increased the number of conf to 6, and I know this is because of the upcoming changes. But for those changes, I am very sure that they have to upgrade their wallet and stuff - imagine the simplest thing. Something goes wrong and you have to download the whole blockchain again? This takes ages, doesn't matter on what kind of connection you are. I would wait 24 hours before panicking. We have witnessed bitstamp being offline for days, we lived through that, I am sure we can live through this.

They do have an issue but with their data center this is what they say. The problem is you are able to ping the website btc-e.com  and traceroute too! so in this case, is it really a data center issue? Just before it went down a sell order was placed worth 414k BTC
The API is working so far