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Код

import java.sql.Array;
import java.sql.Connection;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;

...

    public static void query1(Connection connection, int[] ids) throws SQLException {
        StringBuilder sb = new StringBuilder("SELECT m.mess, m.userid FROM messages WHERE m.userid in (");
        for (int i = 0; i < ids.length; ++i)
            sb.append(i > 0 ? ",?" : "?");
        sb.append(")");
        PreparedStatement ps = connection.prepareStatement(sb.toString());
        try {
            for (int i = 0; i < ids.length; ++i)
                ps.setInt(i+1, ids[i]);
            ResultSet rs = ps.executeQuery();
            try {
                while (rs.next()) {
                    // do something
                }
            } finally {
                try { rs.close(); } catch (SQLException ignore) { }
            }
        } finally {
            try { ps.close(); } catch (SQLException ignore) { }
        }
    }
    
    public static void query2(Connection connection, Integer[] ids) throws SQLException {
        PreparedStatement ps = connection
            .prepareStatement("SELECT m.mess, m.userid FROM messages WHERE m.userid in (?)");
        try {
            Array sqlArray = connection.createArrayOf("integer"/*db spec*/, ids);
            ps.setArray(1, sqlArray);
            ResultSet rs = ps.executeQuery();
            try {
                while (rs.next()) {
                    // do something
                }
            } finally {
                try { rs.close(); } catch (SQLException ignore) { }
            }
        } finally {
            try { ps.close(); } catch (SQLException ignore) { }
        }
    }