Most commentator do not comment on these letters, the exception being the Baal Haturim.
1. The first occurs in Gen 2:4 as the heh of b'hibar'am (when they [the heavens and the earth] were created). The explanation for this is that God created the world with the use of the letter heh and that we should read it as b'heh bar'am (with a [letter] heh he created them) As to why it is small, the Rabbis add that it is diminished as God took the letter from here to give to Abram to make his name change to Abraham (ref) as according to the Baal Haturim the world was created for Abraham’s merit and b'hibar'am is an anagram of Abraham.
2. There is a small chaf in Gen 23:2 in the word v'livchota (and to weep for her [i.e. Sarah]) Baal Haturim explains that he (Abraham) cried only a little because she was old (and thus it was the way of the world).
3 and 4. There are two small kufs. One is accepted the other is in dispute. The first is katsti (I [Rebecca] am weary) in Gen: 27:46 but the second is in b'kameyhem (among their enemies) in Ex:32:25 , however other sources claim that this is not small rather it is odd in that the leg of the kuf is joined to the roof of the letter. Baal Haturim explains katsti as having a small kuf because Rivka foresaw that in the future the temple would be destroyed, the temple being kuf (100) cubits high, hence her assertion that she was weary in her life from the sadness of this vision. The Baal Haturim doesn't comment on the other small kuf so we can assume did not accept it.
5. The most famous small letter is the aleph of vayikra (Lev 1:1) The explanation given, again by the Baal Haturim is that Moses was a very humble man and to he wrote vayaker without the aleph which has the sense of a chance meeting but God insisted that this was deliberate - vayikra (and he called) to Moses. The compromise is the little aleph. However since the nest word el begins with an aleph and in ancient times there were no gaps between words the most likely explanation is that the early scribes did not duplicate the aleph and when the words were split they were unsure of whether to include the second aleph or not.
6. The mem in mokdah (burning) in Lev.6:2 is small.
7. The yud in pinchas (Num 25:11) is also small, however yud being the smallest letter anyway this one can be difficult to detect.
8. Deut 9:24 sees a small mem at the start of mamrim (rebellious) however this is also in dispute. This isn't shown as a small letter in most books but the Baal Haturim explains that this pasuk begins with a mem and ends with a mem to emphise that the whole mem fourty years they were in the desert the Israelites were rebellious.
9. and finally teshi (unmindful) in Deut 32:18 provides another smaller than usual letter yud.
If any reader knows of any other midrashim or explanations as to why a letter is small, then please let me know and I’ll build it into the page.