JO and JA run pretty good in Linux, like most Q3 games as stated before. Besides a few binds being out of whack, installing may be your only real problem. Cedega is a program that'll neatly arrange things into a little GUI for ya', but will cost $15 out of the gate.
Try WineX, and this tutorial on how to install JA will work for JO as well.
http://www.thehaus.net/AltOS/Linux/ht-ja-winex.shtml