You can use any pen with indelible ink. We strongly discourage the use of fancy fountain or ink pens since these tend to leak, especially when people are not used to writing with them. We have seen horrible ink accidents. Choose a trusty medium ball point pen (any color, although many couples prefer black) to give the ketubah the look of a signed document, which is what it is.
We have found that the uni-ball Jetstream Stick Roller Ball Pens, Fine Point, Black Ink work very well and dry quicker than other pens to reduce the chance of smudging.
Helpful Hint: Practice signing your Hebrew names on a different piece of paper before you sit down to sign the actual ketubah (English names also if you need to).