I found myself using tools a lot more in my day to day job this year than I am used to. It is amazing how far some of the software breaking software tools have really come in the last few years. So that being said, I am going to focus on some of the tools that I have found myself using regularly.
Tried and true, Wireshark has been there for me, through thick and thin, since I got into this game long ago. I have used Wireshark for everything from dissecting RIP packets to troubleshooting TLS/SSL connection issues with SOAP Web Services. This tool is an absolute MUST HAVE for anyone in the security field. Be they hacker, hobbyist, or analyst - Wireshark will be one of your best friends.
Cain and Abel
It's interesting - I actually have a Windows XP VM that exists for no other purpose than to run Cain & Abel. This tool is invaluable when you need to capture network packets and have them analyzed and organized in real-time. It is great for sniffing out cleartext credentials (Telnet, FTP, SMTP), and one of the absolute best features is the ability to capture and essentially *bug* VOIP calls.
I remember when I first heard about MSF. I thought to myself, great, a new tool for Skiddies to annoy me with. At first glance it is nothing more than a glorified over-powered version of BO95. However, when you really dig deep under the covers, MSF is more like an IDE (that's Integrated Development Environment for you non-developer types) built specifically for hackers! It is a self-contained runtime where you can discover vulnerabilities and test exploits and shellcode all in a single environment. Really, this is an ingenius tool that's power far exceeds what most people are using it for.
This has become one of the most used tools in my toolkit - I use JBroFuzzer against any new development in any of the applications that I maintain to test Regex patterns, request parameters, cookie values, and more than anything else, RESTful web services. It is amazing how many ways there are to break webservices and with some custom payloads and JBroFuzz you can create some very powerful scans that can be run against your app to dig out even the most obscure bugs that most ordinary testers would never think of.
The quickest way to DoS your own application is by firing up a JMeter test. This is an extremely powerful tool from the Apache team that is written in Java. Load Testing, automated crawl tests, whitebox testing, and much, much more are possible with this extremely easy to use and powerful tool.
The great thing about BS is it is an entire suite of tools that work together and allow you to run a quick (and surprisingly accurate) audit of an entire application. The interface is simple to use and most importantly, it is extendable. It is Java based so it is platform agnostic and works with any browser. One of the cooler features is the ability to suspend and save state then restore and continue later. Great stealth scanning feature.
There are other tools that I find myself using, but I use these almost every day, and absolutely use each extensively when doing an audit. Take this list for what it's worth, but if you haven't tried a couple of these, do yourself a favor and give them a shot.