For the life of me I don't know why it took so long for me to figure this one out but I have finally self diagnosed the pain in my big toe as
Sesamoiditis. For about 10 months now I have had pain in what I always refered to as the big toe joint in my left foot. The pain at times would cause a noticeable limp, particularly if I wore high heels for a long period or was on my feet for awhile and I always have to wear shoes around my house because if I go barefoot for long on the hardwood floor the pain would be bothersome. When the pain first started it was much worse than it is now, but it is definitely sore on a daily basis even though I have grown pretty used to it by now.
Here is what the toe looks like:

A sesamoid bone is a bone found inside a tendon where it passes over a joint. A tendon is a strong band of connective tissue which attaches a muscle to a bone. Your body has several sesamoid bones. The largest sesamoid bone is your patella, or kneecap. The ball of your foot contains two small sesamoid bones, the medial (inner side) and lateral (outer side) sesamoids. These sesamoids act as pulleys for the tendons and help flex or curl your big toe. When you run and jump these sesamoid bones absorb much of your body weight. So my poor little sesamoids have been taking a pounding for quite some time.
Symptoms can include:
Symptoms incude:
-Pain when moving the big toe, especially lifting the big toe up -- Yup
-Tenderness to touch at the ball of the foot -- Definitely
-Pain when walking, running, jumping, or standing -- oh yeah
-Swelling--Maybe slightly but nothing major
Oh and here is the kicker, wearing high heels contributes to the problem. Whaaat? you mean my adorable heels are not good for me feet??? Yeah not so much suprised but I own one pair of flats that are 4 years old and all of my pants and jeans I couldn't wear with flats because they would all drag on the floor. The good news is that I can wear whatever I want to work pretty much and even though I like to dress nicely, I can get away with wearing jeans and running shoes for a little while to help it heal.
The other treatments are:
-a special pad to wear that supports the bones
-a shoe insert that limits the motion of your big toe
-custom-made shoe inserts made for you (orthotics)
-tape your big toe to provide support and limit movement
-a removable walking cast to wear until the pain is gone
-anti-inflammatory medicine
-icing after exercise
-getting a cortisone shot
Obviously some of these are a little extreme in my case. I actually dont experience a great deal of pain while I run but it gets very sore later and standing for a long period of time is more painful. When I run I feel like I stretch my toes as a push off and it actually feels kinda good. Basically ibuprophen, tape and ice are my preferred treatment but if at the beginning of the year I am still experiencing pain I will go to the doc and at least get some orthotics. Right now I have only reached $800 of my $1,800 deductible so I might as wait until next year since I probably won't meet that deductable this year.
Anyway I have dealt with it for this long and even though I have done 2 weeks of almost 30 miles each week and havent had any increae in pain then it isn't getting worse and I can handle it as it is. It is nice to know what it is though!