Ain't ya ev'r herd of compressed air <G>...

Depending on the amount of space you have over the you may be able to sister a 2x something between the pipe.  I've recently used a small angle secured and dapped into the joist in conjunction with 'glulam rivets'.  Notch, hopefully isn't near the support...

Also some codes limit the maximum depth of a notch.  

Did your building inspector flag the work?

Is it causing a noticeable weakness?

Keep in mind the flooring can be a reinforcement, if done correctly. If the area is to be sheathed with plywood, you might consider glueing it down, and using a closely-spaced nailing pattern. You might also consider screws instead of nails.

Actually, notching the top is the correct way to do it.

Here are typical code guidelines for notching:

Never in the center third of the span.
Only in the outer third of the span.
No more than 1/6 depth of joist.

Holes need to be 2" from either edge of joist, the diameter no more than 1/3 depth of joist.

Pg 111,Residental Framing, William P. Spence 1993
Book availiable at 'big box' home improvement stores.

Whether or not you have a problem depends on the joist loading and the notch size, shape and location. Assuming a 'normal' floor arrangement then the guidance given by SteveBausch is fine.  If not then;
If it is a 'normal' floor arrangement and the notches are in the middle third but less than 1/4 of the joist depth then doubling up with joist of the same width and grade as the existing will be satisfactory provided the depth is greater than 3/4 of the existing.
Otherwise get professional advice.

Just for information notches are generally preferred to holes in beams near supports, the maximum shear stress occurs at the middle of the joist.

To add to all the above suggestions: Take a close look at how the contractor over-cut the notches (allow me to presume he has done so). The depth of the notch should be considered equal to the depth of the cut.

-Richard L. Flower, P. E.