Any way to get a faster program start in Unity?

Have you considered installing Preload?

sudo apt-get install preload

Preload is a daemon that monitors the programs you often run and partially loads them into memory. It particularly helps me with heavy programs such as Inkscape.

In my experience it depends on what program you are launching, and in all honesty the perceived difference in start up time is likely just in your head. For example, Midori starts immediately for me, and Nautilus takes sometimes a full minute!

It would help you to run the applications that take a long time to start from the terminal and see what they are outputting, as often times the program does some other things before you see the application window pop up. If the program is taking a while to start from the terminal, and outputs a lot of information, then you would know that it is just doing something extra.

Also keep in mind that it might be a change in the way the filesystem works that causes the delay.