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iCharting: Web, Desktop and Phone Applications for Mood Tracking
updated (maybe for the last time) 9/2012

Okay, okay: now there are bunch of these programs (why did it take so long?).  I can't even keep up anymore. Here are three that seem to have what you might want. The research tool I've tried myself.  The other two seem so simple or well worked out, they've made the list here, but there are more out there I've not examined. Options 2 and 3 are available for both iPhone and Android. 

1. Suppose all you wanted to do was rate your mood every day (not sleep, exercise, or anxiety). That might make it so simple you'd actually do it most of the time!  For that, there's a free simple clean program, web or iPhone (Android "coming soon", as of 9/2012, but they have been saying that for a while...). MoodPanda.   

2. If you want to chart mood and sleep and anxiety, and have your fully private results support a research effort (with daily reminders to chart, which is nice if you need it and can be turned off if you don't) , you want BeatingBipolar.  They have iPhone and Android versions.  You can have your medical provider look at your chart in advance of a visit by sending your log-in info. 

3. However, if you want a full program that's been revised for several years, now very slick, that may be the Optimism program (desktop/laptop, or handheld, Apple or Windows). This is a commercial grade product. I don't know how they are managing to offer this for free (maybe because they're marketing it for clinicians?). 

Again, I'm sure there are others. I'm not staying on top of this evolution! 

 

If for some reason you want to go back to 2010, i.e. the dark ages, to my previous report on all this, here you go: 

Here is a late-2010 assessment by an experienced user. Thank you Cyclothymia. I can't comment on her evaluations because I have even less experience with the products, but you'll find this a useful summary. I have no relationship with any of these companies. 

If you find a really good electronic moodcharting system that's free or costs less than $15, email me please, and if the product looks good to me I will post a note about it here. 

Cyclothymia comments below on:
ChronoRecord           bStable        Optimism products      Moodifi
Medhelp       Android/Blackberry apps         PsychCentral      Moodtracker 

ChronoRecord is only available on the Windows Platform. (I haven't tried it yet.)
 
bStable is now available, for Windows and Mac, starting from $99.  It looks really amazing but I haven't had the chance to try it for real.
 
Optimism is available not only as an iPhone/iPod app, but also as a web client, or a software version for both Windows and Mac for $39.95.  I've been trialing this and while it's reasonably powerful and has the great idea of including common triggers etc., it does not handle mixed states at all! (Kind of a deal breaker if you have mixed states).
There are a lot of iPhone/iPod apps that will do mood tracking but most of them are pretty useless IMO... Moodifi is a reasonable one.  You can take tests that will assess your mood (although tests often don't quite capture your level of psychic pain) -- depression, anxiety and mania, as well as test for functioning, medication and substance.  I actually don't like it much personally, but it has a cool feature where you input the numbers of a friend, family member, your therapist and an emergency number so when you report suicidal ideation it immediately brings up a list asking if you'd like to call someone, and you can just touch the label to call.
 
MedHelp have their own mood tracker (http://www.medhelp.org/land/mood-tracker) which is alright but I don't think it's very well organised visually (I always feel like you should be able to understand a graph very quickly when you look at it).
 
There is also at least one mood tracker for Android phones (http://www.androidfreeware.net/download-t2-mood-tracker.html) and Blackberries (http://appworld.blackberry.com/webstore/content/8741) which at least look alright but I haven't tested them because I don't have those phones.  I figured I'd mention them anyway in case you knew someone who could test them (all of my friends have iPhones!) and so you knew something at lest existed.
The Psych Central Mood Tracker (http://psychcentral.com/quizzes/mood-tracker/index.php) has a really nice visual organisation, but it uses tests rather than human judgement so today it "diagnosed" me as manic when I'm really on the depressed side of mixed (I don't think it does mixed states though).
 
Really the best mood tracker I've used is moodtracker.com -- it's not "pretty" but it's functional enough, handles mixed states, tracks sleep, medication and menstruation, and the visual organisation is reasonable.  Unfortunately I only recommend it because it is a matter of "it sucks less than the rest of the ones I can afford".