Sargeant Seats - http://www.sargentcycle.com/
Corbin Seats - http://www.corbin.com/
Russel Day Long Saddles - http://www.day-long.com/
Rick Mayer Seats - http://www.rickmayercycle.com/
Bill Mayer Saddles - http://www.billmayersaddles.com/
Mr Ed's Moto Seats - http://www.mredsmoto.com/
Rich's Custom Seats - http://www.richscustomseats.com/
Spencer's Seat Mods - http://greatdaytoride.com/Home_Page.php
Biker Cushion Pad - http://www.bikercushion.com/
Alaska Butt Pad - http://www.alaskaleatheronline.com/servlet/StoreFront
Corbin seems to have a love/hate relationship and their coverings are so so. Sargent makes pretty sexy seats that look good with an OK covering. Russel day long are the pinnacle of comfort ugly as sin and the only option for heavy(weight) riders. Rich in Seattle offers ride-in service for a custom fit while you need to ship and reship your seat to get the best fit out of most modified seats. Seat cushions keep you dry and comfortable but they're annoying if they slide around and their looks are mediocre.
You can also modify a seat yourself: http://www.diymotorcycleseat.com/index.php
The above are general thoughts and opinions and rumors read from various forums. What are some other places for modified and custom seats and what are your opinions about them?