There are several of these "suggestions for the new president" sites out there, and its tough to keep track of them all. The main ones I've seen though are:
change.gov
change.org
opposingviews.com

Weather-or-not chiming in on these sites will make a difference, or weather-or-not the ideas will even make it to Pres-Elect Obama, I don't know. However, years of experience have taught me that doing nothing will get you nothing while doing something might get you results.

A post today on American Atheist led me to Opposing Views section on What Should Obama's Priority be After Inauguration?

There are currently 9 main issues listed on the page; 3 are "separation of Church and State" related.

• Religion Root of Problems: Mr. President, Rebuild that Wall!
• Fix Economy by Taxing Churches: An Open Letter to President Obama from American Atheists
• Stop 'Faith-Based' Initiatives: All Forms of Federal Religion Must End

Also looks like these three have jumped to a small early lead in the "thumbs-up recommend" count.

Get registered! And then don't forget to "thump-up" the issues you support. We can't bring change by doing nothing...