I was trying to think of a better way to cover unused vaccum lines for my intake manifold. I was even thinking about filling the holes by welding them shut. ANyone have any other idea's?

The only thing I dont like about those rubber nipples is they get old and break

 

Bondo Marine Epoxy putty stick.
I've used it on the intake, the cooling system, and to beef up weak or broken plastic.

 

you can put high temp RTV inside the rubber nipple. that will reduce chances of it falling/breaking off and even if the rubber cracks or what not should still be ok.

if you have quality vacuum line you can also just loop the lines.

JB weld or what SureShot mentioned would also work fine but is more permanent.