you can use any of them, I would recommend eagle, since its pretty serious and there are tons of tutorials on it ... and once you learn one of the more serious ones you can pretty much use any of them with little change outside of figuring out where stuff is.
as far as missing components go, you can search the interwebs for them, or you can make a schematic symbol for them. No matter what you use its going to be missing something, thats the way it is. Parts are obsoleted every day, and manufactures are releasing new parts heavy and frequently.