Tools I use:
HeidiSQL (when using Windows)
SequelPro (when using a Mac)
MySQLWorkbench (both Windows and Mac)
JetProfiler (free version which has limitations)
Diffing tool (I use a few different ones, Xcode on a Mac has one called "FileMerge")
Text Editor (I like Sublime)
PuttyManager for when I'm on a Windows system (MTPutty)
Box.com RainGauge
Box.com Anemometer
Various Command Level Tools (sysctl, top, vmstat, iostat, mpstat, lsof, df, netstat, pidof, flock)
MySQL command level Tools (mysql, mysqladmin, mysqlbinlog)
Percona Toolkit (online schema change, digest, deadlock-logger, heartbeat, stalk...)
Trend tool with charts (Zabbix, Ganglia, Cacti, etc)
Alerting Tools (Nagios, Zabbix, etc)
Custom tools (Bash Scripts, PHP scripts)
Monitoring tools for clusters (I don't have a tool for this yet as I'm still working on setting up Galera clusters and we don't use NDB cluster)
Many of these tools are for more than just monitoring but mot allow so little bit of monitoring that comes for free. I didn't realize how spoiled I was as an Oracle DBA with Enterprise Manager that does most of what was needed in one tool.
You may notice that all of the above tools are FREE.
I've done evaluations on paid monitoring tools with MonYong, MySQL Enterprise Monitor, and VividCortex. It is impressive what these tools can do but I don't have the budget to pay for them. I really like how JetProfiler does profiling and I've love to have tool that can profile constantly and keep that info for a long time like VividCortex. I really like what Box.com's anemometer can do in this regard but it still didn't perfect and required a number of other tools to make it all work. MonYog's profiler has some similarities to JetProfiler but not as good for profiling and their tier 2 support was located across the globe and slow to respond to my requests.
One of the things I really liked with MonYog/MySQL Enterprise monitor is how it tracks config variables and automatically recommends performance improvements and provides security warnings. I also liked how easy it was to compare configs from server to another in MonYog.
Oracle's MySQL Enterprise Monitor did a good job of tracking metrics but I thought the graphs were too hard to read, probably I had just gotten so used to reading charts in Cacti that I thought the Oracle graphs were kinda weird. Oracle has good alerting, as does MonYog but I didn't need it because we already have a tool for that using Nagios.
VividCortex is pretty good but I'd like to see it include the same features that JetProfiler has. I really like Box.com's anemometer and Box.com's rain guage but they are open source software that you have to setup and manage yourself and procuring resources is difficult. I think VividCortex has come the closest so far to combining them all into one tool but at this point, I'm not really happy with any of them and so I have to run a dozen separate tools to accomplish what I want. And then for SQL Server and MongoDB and other NoSQL solutions I have separate monitoring solutions. Also, the licensing is too expensive when your company setups MySQL instances like crazy so even if one tool met all the requirements, I don't think I'd ever get a purchase order signed to use it across the board meaning I'd still have to use lots of different tools. Percona has made a number of enhancements to MySQL in Percona Server which MonYog has done a good job of including in their monitoring metrics but I haven't seen that in other monitoring tools.
For MySQL some of the things I'd like to have in a tool
1. Box.com rainguage to track how often and all the metrics associated with a specific type of event happens
2. Box.com anemometer to track historical trends for specific queries
3. Trend analysis tool like Zabbix/Cacti/Ganglia for seeing historical trends of the OS/MySQL counters
4. Profiler tool like JetProfiler but one that is always on
5. Custom tools we created to track config changes, sizes, row counts, compare changes
6. Various command level tools
7. MySQL workbench to do admin type of work
8. Want to be able to monitor galera clusters
9. Want to be able to monitor Percona specific additions
10. Want to see currently locking/blocking queries like how Oracle Enterprise Manager does it for Oracle databases
11. Want the tool to keep track of the size and count of all my tables and tell me how much they grew or changes day by day, week by week, month by month
12. Intelligent recommendations telling me where I'm missing indexes, which queries need tuning
13. Tracking of which queries I've already reviewed and don't want to see anymore in the profiler, a history showing when the last time I reviewed this specific query