Since my post that briefly covers Dwarf Therapist for Dwarf Fortress seems to be receiving a lot of hits lately I thought I should take it a step further and post a more comprehensive guide.
Getting Started
First of all you need to make sure you have it installed, go grab it from here. At the moment it is supported on Windows and Ubuntu/Debian Linux systems, to get the Linux version head here instead.
Once you’ve got it downloaded just extract the archive somewhere sensible and fire up the DwarfTherapist.exe file include. This guide will focus on the Windows version, the interface and functionality is the same but the installation steps are slightly different (basically, if you need help installing the Linux version I’m saying you’re on your own 🙂 )
Main interface
Ok, so if you have dwarf fortress already up and running then Dwarf Therapist will connect 
to it automatically (connect = picks up DF running in memory). On the main screen you have  a toolbar running along the top of the program with options such as connect to DF, read dwarves, expand all and so on. I will step through each one in turn so you have a good idea what they do.
Connect to DF – Use this if you started Dwarf Therapist before Dwarf fortress or if you didn’t have a game running in Dwarf fortress before loading Dwarf Therapist. This will set it up to connect to your game. If you have any issues, make sure you have the latest version. Due to changes in the game it can sometimes take a week or so for the developer to get a new version out the door.
Read Dwarves – So the screen you see on load isn’t actually dynamic, it will display the latest information since it last read your game. To force an update hit this button. This can be useful to quickly check on happiness levels or to see if changes you have made within the game have taken properly.
Expand All / Collapse All – This just expands or collapses the options below the toolbar, if you have your dwarves grouped (we’ll look at this later) by happiness for example, hitting collapse all will just collapse the view to a list of different happiness levels within your fortress and a count of the number of dwarves within the group.
Clear Pending Changes / Commit Pending Changes – So like I said above, this program runs a little statically in that you need to read dwarves for updates and in the same way you need to push any changes out to your game too. Once you’ve made some changes (we’ll look at that later) you hit Commit pending changes to send it over to the game, hitting clear does pretty much what you would expect – clears any non-committed changes 🙂
Options / Exit / Scan memory – Options is pretty obvious, I’ve never used it but feel free to have a nose around to see if there are any settings you want to change (such as colours). If you need me to explain the exit button you probably want to attend a college course before trying Dwarf Fortress :). Scan memory is an advanced option for people looking for specific things within their game world – I have never used it.
Down the right you have a panel for your pending changes (the ones you haven’t committed yet) and another panel for any custom professions you create. The great thing about the custom profession panel is that you can basically create a series of templates for your dwarves that include specific skills enabled so you can really strongly control what new dwarves or grown children start to learn.
The Dwarves Panel
The dwarves panel kinda consumes most of the program, in the screenshot below I have cropped out the rest of the interface so you can get a good look at the dwarves list. Again its all 
fairly self explanatory. Running down the left is the title of each group and the names of all of the dwarves within that group. Along the top is a list of the professions/skills and then at the intersection between dwarf and skill is a square that indicates how skilled that dwarf is in that area. If a dwarf has a skill enabled then the square will be purple in colour, within the purple square a small square will start to grow based on their experience. As this square grows to fill the purple square it will eventually change into a diamond. This 
is just a neat way to visually show how experienced a dwarf is, to see exactly how experienced they are just hover your mouse over the square and it will give you a tooltip with the details. In the screenshot to the left my mouse pointer appears to have vanished, but its actually pointing at the white square to the top left of the tooltip 🙂
If you click on a square that isn’t currently purple you’ll notice it turns purple. This is how you enable labours for your dwarves, easy huh? All you need to do is hit commit and your dwarf in-game will start to do that labour (unless it requires a tool, in which case they will go grab a spare tool and then do it 🙂 ). In the same way you can also disable a labour by clicking on a purple square and then committing it. The beauty of using Dwarf Therapist over the in-game GUI is purely because you can instantly see people with high experience levels in un-enabled labours, this can happen over migrations or as children grow up. In the same way you can see which dwarves don’t have many or any labours enabled.
I don’t feel there is much more I can explain about this screen really, that’s essentially the bread and butter of the program (although feel free to post a comment if you think there is something you’re missing).
My tips would be to get a couple of dwarves set up as nurses. Perhaps 1 nurse per 80 dwarves, all you need to do is remove all labours except for the recovering wounded and feed patients ones. Personally I tend to enable all of their medical labours to get them trained up, they might be a bit crap at first but if you suffer a major attack it does help to have these skills spread across multiple dwarves.
The Military Tab
Finally, there is a military and social tab. I never use the social tab, its a bit redundent in my opinion as the in-game GUI is pretty good at highlighting dwarves with 
appropriate social skills for jobs, its not something you can just enable or disable. The military tab is great for keeping checks on any high skill levels slipping into your fortress over migrations, keep checking here and make sure you get them into a squad in the game as soon as they appear.
I hope this has helped some people out there! Feel free to leave a comment if you have any feedback, comments or just to complain about bits :). One final warning, once you start using this you will become entirely dependant on it, so don’t say you weren’t given fair warning. Happy Mining!