How does performance of SQL Server CE and SQL Server Express compare? We have an application that runs on netbooks. It currently uses a SQL Server CE 3.5 database, and we are thinking of upgrading to SQL Server Express.

Just wonder if there are any benchmarks to compare the performance of SQL Server CE and SQL Server Express? Would it be too intensive for an atom netbook?

We are using SQL Server CE 3.5 and we are thinking of moving to SQL Server Express 2012.

UPDATE:
Why are we wanting to upgrade? Because we will now be using merge replication with the SQL Server Express database.

Also we don't want to limit ourselves. We might use stored procedures and triggers on the database because with the replication solution we will be redesigning parts of our system.
For your case and reasons to upgrade

merge replication is available in SQL Server CE 3.5

Stored procedures, views, triggers is not available in SQL Server CE 3.5

for a basic comparison between the 2 editions in your case working on a net book

1.
SQL Server CE 3.5 can Runs as in-process with application
SQL Server Express runs as a service

2.
SQL CE supports maximum size of 4GB
SQL Express can go up to 10GB

3.
SQL CE Doesn't Support FILESTREAM
SQL Express Supports FILESTREAM


Procedural T-SQL - Select Case, If, features is not supported in SQL CE
Procedural T-SQL - Select Case, If, features is supported in SQL Express


5.
Distributed transactions is not supported in SQL CE but supported in SQL express


Native XML, XQuery/XPath is not supported in SQL CE but supported in SQL express


7.
Stored procedures, views, triggers is not supported in SQL CE but supported in SQL express


Role-based security is not supported in SQL CE but supported in SQL express


9.
concurrent connections supported in SQL CE is limited to 100 but unlimited in sql express

this is a useful blog focused on sql CE 

for the comparison between the 2 in your specific environment you can use these tools

SQL LOAD TEST
SQL STRESS TEST TOOL

and check this post on SO about sql statment performance
https://stackoverflow.com/questions/1555471/what-tools-are-available-to-test-sql-statement-performance