The System.Data.Objects.SqlFunctions has (AFAIK) all the useful T-SQL functions like Difference, Soundex, Like, etc.
These functions are translated in where clauses by Linq2Sql into their T-SQL equivalents.
EDIT: Whoops, that's 4.0. Sorry about that. That said, to do so you can create a user-defined function in your database, and add that function to your DBML file and call it just like you would SqlMethods.Like (which is the one I was thinking of). Here's the MSDN docs on it.
Basically you just create a UDF that takes the same inputs as DIFFERENCE and returns the same results. That function does nothing but call the DIFFERENCE method. Then you expose that in your DBML, and use your function in your queries.