My children use to be scared of doing number two's in the toilet as well.  I use to place them on the toilet and they use to hold it in with tears falling down there face.  So I got them off the toilet and put a nappy (gave in) and they did it in there nappy.  A few weeks later I didn't give in and they wanted to get off and I kept asking them questions and they were saying they were scared.  I reassured my children that it will be ok and they are big now and they didn't need to wear nappies anymore and then next minute it magically happened.  They felt so relieved and so did I :) 

Stephen lost the plot one day with a very stinky #2 accident... He told Jaydee that he just couldn't take it anymore and offered to pay him a gold coin each time he did it in the toilet.  Jaydee loves filling his helicopter money box, so he was very excited and most agreeable. 

We also told him that if he had an accident, he would have to pay Mumma or Daddy to clean it up.  Well, he went ok, he only had a couple of accidents, as he wasn't too pleased about having to pay us.  Within a couple of days, the problem was solved!  It's funny though, his uncle is in the habit of emptying his pockets out in the bathroom and leaving change by the basin.  Jaydee is getting a very full money box, as he is continuing to help himself to payment after he finishes on the loo ; )

You could find an alternative form of 'payment' like stickers, stamps, cheap little cars from the $2 shop.  We found it to be very fun and very effective with Jaydee who is almost 3.

I have found with my three old when it came to toilet training. And he is fully toilet trained now, what I done was I went out and got whole lot of hot wheel cars, and then each time he sat on the toilet, I show him,and said if he did a number two the toy was his, but only if he did the number two. It my take a couple of times to do it, but keep at it. he will get the hint on what he has to. even if you get his brother to do the same thing. It will put a smile on his face and yours.I hope this will help.

I am in the same situation.  My twins are nearly 4.  my daughter is excellent at toileting, whereas my son wees in the toilet maybe 90%of the time (he still has the odd accident) but still poos his pants.   Its so frustrating having one twin that can do something, and the other beng really bad at it.  He is gradually improving, as he used to have a fear of pooing on the toilet, now at least he goes sometimes.  I think he poos his pants when it is going to be a particulary big and difficult one to push out, as he likes to find a nice quiet corner to concentrate.  We tried a sticker star chart on the toilet wall (the idea was that every time he got to 5 stars, he would get a present).  I also had a photo of him sitting on the toilet stuck to it- for a bit more visual encouragement.  That worked a bit.  I think its mostly just time.  He will get it in his own time.  I know that whenever Lachlan disappears into the play room and tells me to go away, that i need to encourage him to sit on the toilet.

good luck.  (if you find anything that works 100%, let me know!!)