The first thing I would do is contact whoever is in charge of your travel. Find out if they will let you pick one airline and stick to it.

If that doesn't work, then there's no way of pooling all the points together into one program without a significant loss of miles.

For the majors, here are the combinations where you won't lose any miles.

American
Continental/Delta/Northwest
United/US Airways

If you're being booked on LCCs, I doubt there is a way to pool those miles/credits. Alaska flights can be credited to American, Continental, or Northwest.

Good luck on getting your travel arranger to change their ways.