I'm currently using Google Chrome, and I must admit that it suddenly stopped being as laggy as it used to be, and now just seems to have lag when you move a zoomed in map with objects on it.

A couple things to consider:
I'm guessing you tried to make the units that you place on the map be accurate in size according to the size of the map(?) and while nice, it does make it difficult to see when you are completely zoomed out where certain objects are. For example, I was putting marines down on a fully zoomed out map and I could barely see them.
When you attempt to put multiple objects down on a map in quick succession (such as marines) it can cause the map to zoom in (I think because you zoom in the map on double clicks).
When I attempted to clear the entire map, I ended up using the delete phase button because I couldn't find a delete all objects button. This brought me to phase 0/0 (I was on phase 1/1 before deletion), and I had to create a new phase in order to draw or place items on the map. Not sure if this was intentional or not, but it was slightly annoying.
It would be really nice to have zoom based on scroll wheel (I know you said something about adding mouse integration later, but I just wanted to make sure you knew that this is probably the most important thing on my list in terms of development, so why didn't I put this first? I have no idea).
These things are all really semi-small issues, and I would like to say that I really do enjoy your site, and think that it would be incredibly useful (especially if you can keep adding more and more games onto it). I would like to say congratulations on a great site, and I'll let you know if anything else seems amiss to me! :D