Cooler Master CM 690 II Advanced has eSATA and two USB2 ports on the top/front panel. I believe the Rosewill Blackhawk has quite a close relationship to this particular case. Don't know if that speaks to the build quality.
CM Storm Scout has 4x USB2 ports on the front/top as well as eSATA.
CM Storm Enforcer has 2x USB2 and 2x USB3.
Enermax Hoplite, 2x USB3 and eSATA.
Enermax SpineRex 1x USB3, 3x USB2 and eSATA.
NZXT H2 Classic 3x USB2, 1x USB3. Easily accessible dust filters.
Xigmatek Utgard has 2x eSATA ports and 4x USB2.
A few keyboards I've seen have had some extra USB ports on them, don't know if you want to explore that as a way to reduce clutter on your desk.