Everytime I JB my iPhone after a couple of days it starts to get very noticable lag when I open apps and scrolling and a few other things.

I have winterboard, Notifier and a basic theme.

Why does my iPhone always have lag or is it part and parcel of jb'ing?

Some of it has to do with Jail breaking the phone.
But most of it has to do with the number of apps your running.
Stuff like winterboard does put a heavy price on the limited iphone resources.

There is a huge debate on this subject use the search button.