Personally, I like to install minor programs (games, simple apps) onto my card just to keep space on the phone for stuff that might actually need to be installed on there. Programs like TCPMP, with its many tendrils that reach into the phone to give it extra functionality like YouTube, I will install completely on the phone. This is someone coming from a Q though, so I don't know what to do with all this internal memory.
But as for if it matters, that I guess really depends on the program. I've seen some programs that explicitly say you MUST install on the phone for them to work properly. My take on this is that if it doesn't have that disclaimer, it's really up to you.