You aren't going to get a real answer with a question with this. All you're going to get is bios'd opinions.
Here are my opinions ordered by volume
Cryptsy has been open for a long time with no major breaches besides some bad code issues. The volume and user count makes them a huge target for attackers and they have held up.
Mintpal has done a great job as well and has kept users funds secured the entire time.
The above exchanges are where the major volume is for altcoins.
Next on my list would be bittrex and poloneix for volume
Bittrex has admins readily available almost all the time in IRC and have continued to make improvements to their site while keeping users in the loop, they are also a registered business and also have their personal names listed on their site. They have kept coins secure so far.
Poloneix has good volume but has also already had 2 breach incidents that could have been easily avoided. Hopefully there is no 3rd times a charm.
atomic-trade - lacks a huge amount of volume but has done a lot of work and dropped a lot of money to get the FICEn certifications which only are needed if you offer USD which they do. They beat Cryptsy to the field with this feature. Advertisement capchas are a huge turn off and i somehow got into a capcha/advertisement loop while trying to reset my password. Owner also has his personal information out there.
C-cex - don't know much about it other than they lost some coins at some point and are paying them back.
CryptoALTeX - Well I own it so its obviously amazing
. My personal information is available by googling my screen name and I'm also a registered LLC and explain my security procedures/other things in the About page on our page. Lacks volume
There are others I've missed but I wont' comment as i don't have an account there or have not used them.