Would it matter if the Earth rotated clockwise?

Barring whatever fantastic energies would be required to stop the mass of the Earth from rotating and then changing the direction of the rotation, one of the major things I can see changing would be the expectations of weather patterns.

Part of what affects our weather is known as the Coriolis Effect.

While there would certainly be effects from the change of the weather from the Coriolis effect how this would change the weather could only be guessed. It is certain to be transformative, and if it were an abrupt change, possibly catastrophic as deserts might move, food crops might be affected, and likely expected storm patterns would be changed.

Edit:

I neglected to think about the effect this would have on our structures which would collapse due to shearing action unless the stopping action included a planetary stasis field. Objects in motion tending to stay in motion and rotation speeds of over 1000 mph and the inconvenient theory of conservation of momentum. I forgot to think about our oceans as well, since the Coriolis effect would change them, too.

I also neglected to consider the molten core of the Earth (pesky spinning, geo-magnetic iron). Stopping the rotation of the molten core might cause the magnetic field of the Earth to collapse, allowing the world to be bathed in cosmic radiation (killing every living thing).

My assumption was when they stopped the rotation of the Earth and reset it, they would consider having a magnetic field a good thing and would be sure to stop reset the whole thing. Granted, the Earth of the year 3000 may have other advantages which might offset any changes from the altered rotation of the Earth. As a funny idea, it has potential, but the serious ramifications of such a feat boggle the imagination.

The day/night cycle is the first obvious effect: Days and nights would both be longer (EDIT Or shorter, apparently I got it backwards) if the speed of rotation is the same.

All life on the surface of the planet has evolved for day/night cycles of roughly the length we experience now, with leeway for the difference between summer and winter. A sudden change is likely to affect the health and/or sanity of most species on the planet, although it may not be apparent at first.

The planet's rotation and the tides are also connected, as noted by Thaddeus in his answer. If one is affected, the other is likely to be as well. Again, I'm not a physicist, so it's difficult to theorize the net effect.

Both the change in sunlight and the possible change in the tides would affect coral reefs, which seem to be sensitive to both. If the change is bad enough, the effects could bubble up to mass extinctions in the ocean.

Don't forget, you're also screwing with the molten core of the planet. If you make the surface spin one way, and the core slows down, our Magnetosphere could break down entirely, which allows the solar wind to just blow away the ozone layer - and if that happens, the surface of the planet would be exposed to extremely dangerous levels of UV radiation, causing mass extinctions.

A change in the direction in which the Earth rotates would cause a heap of changes. The magnetic field (or the geomagnetic field) generated by the motion of the molten iron alloys in the Earth's outer core would flip poles, meaning the magnetic north pole and the magnetic south pole would 'switch'.

The Earth uses its geomagnetic field as its means of protection from solar winds (energetic charged particles emanating from the Sun). With a change in the geomagnetic field, Earth's defense to these solar winds may be hindered. If solar winds were permitted to reach Earth, they would strip away the ozone layer and expose Earth to harmful UV rays. Furthermore, the vast majority of technology now-a-days utilizes these magnetic fields and a change in these would shut technology down (what would we ever do...). Also the Coriolis effect would be thrown way off kilt. This would cause dramatic changes in weather and possibly natural disasters in areas in which they are not common to. Hope this answers your question. The big change in my opinion would be the geomagnetic field 'switch'. This could lead to mass extinctions for many species.