You can resolve the issue by forcing the collation used in a query to be a particular collation, e.g. SQL_Latin1_General_CP1_CI_AS or DATABASE_DEFAULT. For example:
SELECT MyColumn
FROM FirstTable a
INNER JOIN SecondTable b
ON a.MyID COLLATE SQL_Latin1_General_CP1_CI_AS =
b.YourID COLLATE SQL_Latin1_General_CP1_CI_AS
In the above query, a.MyID and b.YourID would be columns with a text-based data type. Using COLLATE will force the query to ignore the default collation on the database and instead use the provided collation, in this case SQL_Latin1_General_CP1_CI_AS.
Basically what’s going on here is that each database has its own collation which “provides sorting rules, case, and accent sensitivity properties for your data” (from http://technet.microsoft.com/en-us/library/ms143726.aspx) and applies to columns with textual data types, e.g. VARCHAR, CHAR, NVARCHAR, etc. When two databases have differing collations, you cannot compare text columns with an operator like equals (=) without addressing the conflict between the two disparate collations.