Of course, my favorite of the two would be HBO. As of lately (past 2 years), Showtime has been getting points in my book. They both have pros and cons that seem to offset each other, but I guess that what keeps me watching both programs...
HBO:Pros1. Has a better setup, great screen resolution
2. It appears to be a bigger network (dont quote me on that)
3. Better commentators
4. Better fighters
5. Better promotional material (Road Block, 24/7, Ring Life, Face-Off)
Cons:1. Commentators have the tendency to have man-crushes, be nuthuggers, or simply gravitate towards the more popular fighters (not in that order).
2. Sigh...cant think of anymore at the moment...
Showtime:Pros:1. The commentators dont nuthugg or have extreme man-crushes...they call the fights just as they go.
2. Most of the fights end in TKO/KO or end controversially...which is good for viewers!
3. Showtime fighters seem to be hungrier
4. Their fights have more undercards than HBO.
5. If a fight ends controversially, their staff dont hesitate to right at it (Jim Grey especially

)
Cons:1. Of course the picture isn't as clear as HBO
2. Commentators aren't as live as HBO