Enable query store for all databases
In both cases for the attempted queries in the question, the problems are simply syntactical.

In the first case: You have an IF condition, but do not group the statements after it together, so only the statement immediately following the IF is conditional. The second ALTER DATABASE statement always executes. To fix, do this:

EXECUTE master.sys.sp_MSforeachdb N'USE [?];
IF DB_ID() &gt;= 5
BEGIN
  ALTER DATABASE [?] SET QUERY_STORE = ON;
  ALTER DATABASE [?] SET QUERY_STORE
   (OPERATION_MODE = READ_WRITE,
    INTERVAL_LENGTH_MINUTES = 30,
    MAX_STORAGE_SIZE_MB = 1000,
    QUERY_CAPTURE_MODE = AUTO);
END;
';


You probably also no not need the USE statement. It could be removed and then the DB_ID() could be changed into DB_ID(N''?'').

In the second case: You did not escape the embedded single-quotes. You also had an extraneous EXEC, and you did not include the msdb system database. To fix all of that, do the following:

EXECUTE master.sys.sp_MSforeachdb N'
IF (N''?'' NOT IN (N''tempdb'', N''master'', N''model'', N''msdb''))
BEGIN
   ALTER DATABASE [?] SET QUERY_STORE = ON;
   ALTER DATABASE [?] SET QUERY_STORE
    (OPERATION_MODE = READ_WRITE,
     INTERVAL_LENGTH_MINUTES = 30,
     MAX_STORAGE_SIZE_MB = 1000,
     QUERY_CAPTURE_MODE = AUTO);
END;
';


PLEASE NOTE: @Kris is not incorrect in saying that "sp_MSForeachDB is undocumented and unsupported", and the advice to use another mechanism to cycle through DBs is good advice. It might not be worth the trouble if this is a one-time task, but if this code is to be used repeatedly, then yes, you should probably heed that warning.