Here's the first 2 I did.
 
Gas properties (40 minutes) 
 
1.	Scroll for small particle not working 
2.	After you have more than 100 of either species in the container the scrolls act irregularly; the curser jumps between spots

These are present  also in version 3.05, the one from the install disc from March I am not familiar with what might be on the "to do" list so I just looked for everything.
3.	If you already have particles in the container, you cannot change the amount by highlighting and typing. 
4.	If you Pause, decrease the size of the container and then step or Play, the particles do not stay in the container. 
5.	When you Reset if you are Paused, the thermometer and pressure gauge do not zero until you Play, the particles are zeroed and the volume returns to default settings. The features on the control panel don’t reset, but I think we had agreed on that. 
6.	If you put in a lot of particles, quite a few escape the container through the walls  (around 300 becomes noticeable) My students made a game of this, by the way. 
7.	Personally, I am not sure that I understand the model for gravity. I haven’t used it in class and my P Chem (lack of) is showing. Why does increasing the gravity increase the pressure and temp?
 
Reactions and Rates (25 minutes) 
There are many known bugs and they are documented in Ron’s comments. I am familiar with them so I just looked for things that were not present before.

First Panel
1.	The shooter doesn’t work if you change the type of reaction until you hit Pause then Play, but the particle is given a relative amount of energy based on how much you moved the mouse.
Rate experiments panel
2.	The Strip chart is not working when you Begin an experiment. You can get it going like using the pump or changing the current amounts. 
3.	The Begin/ End experiment seems to be acting irregularly. Sometimes I had to wait 10 seconds for the experiment to restart. I acted like an idiot for a while pressing them too quickly. Then it occurred to me to wait a while (much longer than I have the patience for) 
4.	I said I wasn’t going to mention any documented things, but I would like to prioritize having a fixed size for the Pie chart. I know we talked about this in a PhET meeting and it is distracting.