Yeti_C has handed responsibility of clickable maps development over to sherkaner. The most recent installation details can be found in this thread.
<update 7 (Twill)>
Edthemaster, the original developer of this thread has gone on (hopefully) temporary walkabouts.
Yeti_C has taken on the bug squashing task in this post
The most recent Yeti version is at http://userscripts.org/scripts/show/32305 but hopefully ed will return to pick up his fantastic script.
WARNING Version 3.21 below will NOT work on some maps due to recent changes! Use the script above.
<UPDATE 6>
Version 3.21
http://userscripts.org/scripts/show/13824
-[feature] no more worrying about what order the scripts are loaded!
-[feature] army counter now appears over teammate territories, too.
-[feature] auto-attack[x]. (see user guide under 'special attacks')
-[feature] auto-advance. (see user guide under 'special attacks')
-[feature] color-coded from-markers and outer border of the map to easily distinguish between phases. option to toggle map border between thin, thick, and off.
-[feature] changed how script refreshes (it's faster and more reliable now)
-[feature] 'refresh map' hotkey
-[feature] added id property to all image elements and army counter (to make them easier for other monkeys to find, all image ids start with 'cm-')
-[fixed bug] from-marker goes away now after winning a game
-[feature/fixed bug] confirmation settings for deploy, phase end, and auto-attack are not available from the clickable maps menu if BOB is running (to prevent conflicts/double-confirmations)
-[feature] to prevent conflicts with BOB's hud, the floating action menu is not available when BOB is running
-[feature] close [x] is always visible when viewing the user guide
-[fixed bug] mousing over the map in a spectator game no longer causes errors
</UPDATE 6>
<UPDATE 5>
Version 2.4
NOTE: Before installing this version, please delete the previous version(s). Otherwise you will have two Clickable Maps scripts running at the same time and stuff won't work right

With this version, Clickable Maps now works with the site XML update.
http://userscripts.org/scripts/show/13824
- [feature] mouse wheel only increases/decreases armies if over map. otherwise it will scroll the page as usual
- [feature] added user guide
- [feature] checks BOB's confirmation settings so that confirmations for a given action are only enabled for one script at a time.
- [fixed bug] site xml updated caused script to stop working
</UPDATE 5>
<UPDATE 4>
Version 2.2
- [fixed bug] clicking too fast disables script until page is reloaded
- [feature] cursor changes to hourglass while script is processing
</UPDATE 4>
<UPDATE 3>
Version 2.1
- [feature] re-added shift-click for auto-attack and fortify-to
- [feature] option to turn off floating army quantity indicator
- [feature] added "begin turn" hotkey
- [feature] option to choose between right-click or left-click to deploy 1 or deploy selected
</UPDATE 3>
<UPDATE 2>
Happy birthday CC! Clickable Maps version 2.0 is now available at http://userscripts.org/scripts/show/13824.
IMPORTANT NOTE FOR BOB USERS:
- * After installing this script, right-click the Greasemonkey icon in the bottom-right corner, select Manage User Scripts..., and make sure BOB is above Clickable Maps in the list on the left. Otherwise the new Clickable Maps visuals (cross hairs, friendly marker, advance marker) may not show up on the map, and BOB's Map Inspect feature may not work properly.
* Also, on some maps, if the Map Opacity is set to 100%, then the new Clickable Maps visuals may not show up either. I suggest setting the opacity to, at most, 70%; if you experience this problem, that is.
* If any of you coders out there can figure out a way around either of these issues, I'm all ears!

Again, thanks to all who provided feedback, sorry to those who had problems with the last version, and please keep the feedback coming!
Here's a list of changes in this version:
- [feature] improved help (again). tool-tips appear with simple instructions when mousing over the map (option to turn off)
- [feature] frienldy attack-from/advance-from/fortify-from marker (option to turn off)
- [feature] advance-to marker (option to turn off)
- [feature] confirm phase end (option to turn off)
- [feature] automatically check userscripts.org for updates once per session, and a 'Check for Updates' menu item.
- [feature] customizable hotkeys, option to disable hotkeys
- [feature] quantity indicator appears when territory is moused-over during deploy, advance, and fortify phases
- [feature] right-click for auto-attack and fortify-to
- [feature] tooltips appear when a territory is moused-over to show what will happen when clicked (ie. "Advance 6" or "Deploy 32") (option to turn off)
- [feature] crosshairs appear over attackable enemies (option to turn off)
- [feature] condensed, categorized menus
- [fixed bug] sometimes an error displays when trying to switch from one attacking, friendly territory to another
- [fixed bug] advancing does not work if player attacks without clicking the map
- [fixed bug] cannot chat during your turn because the 'e' key is used to end phases (all hotkeys are now ignored while chatting)
</UPDATE 2>
<UPDATE 1>
New version: 1.0
New features
* Improved help
* Options menu to turn on/off confirmations, etc.
* Option to use mouse wheel to select number of armies
* Auto-attack function
* Option to deploy 1 army per click
* "Intelligent" clicks: clicking on any friendly territory automatically sets that territory as the attacking territory, and clicking on an enemy (without having to hold SHIFT) automatically attacks that territory.
Thanks to all who provided feedback and, as always, keep the feedback coming!
</UPDATE 1>
With this script you can click the map to select the territory you want to deploy to, attack from/to etc. It could probably still use some work, but I wanted to post an early release so people can try it out and give me some feedback for improvements.
One thing in particular I was looking for feedback on is the fact that the action menu now floats at the top of the screen so you don't have to scroll down to see what territories or how many armies are selected on larger maps---but I can see how it might be annoying so please let me know if it is.
It was tested alongside BOB with no apparent issues (but I wasn't paying as close attention to BOB, so if anyone finds that it breaks BOB, please let me know).
Here's the link to install it: http://userscripts.org/scripts/show/13824
PS: Thanks to the authors of BOB for a few code snippets
