I'm really surprised at how this free tool from mysql.com seems to be slipping under the radar.
I've been a cocoamysql user for some time -- and while cocoamysql is a nice tool, it hasn't seen development in eons and it has a lot of limitations.

Mysql.com is obviously gunning to make MySQL Query Browser a top notch tool and it is equal to or better than every other mysql query tool I've tried.

This app is far closer to the advanced functionality of an app like safari, note that you can:
run multiple queries in tabs
keep a query history (that spans days)
bookmark queries

to name a few similarities.

Here are a few other features that are worth noting:
The entire mysql reference is built right into the app. sweet.
You can compare resultsets [ run two queries and it'll highlight line by line the differences between them], very cool.
it highlights tablenames/column names as you type the query so you're not always trying to guess what you named the 8th column in your six table.

While it has a few interface quirks (run a query, then select 'Explain Query', now select 'Explain Query' again, and again, now try to get rid of any of those panes -- or type a query that doesn't work, it'll disappear) I'm going to peg this at 5 stars as the best free tool I've seen for mysql yet.