Global comments query:
EXPLAIN SELECT n.nid, n.title, n.type, n.changed, n.uid, c.timestamp AS last_updated FROM comments c INNER JOIN node n ON n.nid = c.nid WHERE n.status = 1 AND c.status = 0 AND 1 ORDER BY last_updated DESC LIMIT 0, 1000;
+----+-------------+-------+------+----------------------------------------------------+----------------+---------+-----------------+------+-------------+
| id | select_type | table | type | possible_keys | key | key_len | ref | rows | Extra |
+----+-------------+-------+------+----------------------------------------------------+----------------+---------+-----------------+------+-------------+
| 1 | SIMPLE | c | ref | lid,tracker_global | tracker_global | 1 | const | 359 | Using where |
| 1 | SIMPLE | n | ref | PRIMARY,status,node_status_type,nid,tracker_global | PRIMARY | 4 | fk_portal.c.nid | 1 | Using where |
+----+-------------+-------+------+----------------------------------------------------+----------------+---------+-----------------+------+-------------+

Global nodes query:
EXPLAIN SELECT n.nid, n.title, n.type, n.changed, n.uid, n.changed AS last_updated FROM node n WHERE n.status = 1 AND 1 ORDER BY last_updated DESC;
+----+-------------+-------+------+----------------------------------------+----------------+---------+-------+------+-------------+
| id | select_type | table | type | possible_keys | key | key_len | ref | rows | Extra |
+----+-------------+-------+------+----------------------------------------+----------------+---------+-------+------+-------------+
| 1 | SIMPLE | n | ref | status,node_status_type,tracker_global | tracker_global | 4 | const | 222 | Using where |
+----+-------------+-------+------+----------------------------------------+----------------+---------+-------+------+-------------+
1 row in set (0.00 sec)

User nodes query:
EXPLAIN SELECT n.nid, n.title, n.type, n.changed, n.uid, n.changed AS last_updated FROM node n WHERE n.status = 1 AND n.uid = 1 ORDER BY last_updated DESC;
+----+-------------+-------+------+---------------------------------------------------------+--------------+---------+-------------+------+-------------+
| id | select_type | table | type | possible_keys | key | key_len | ref | rows | Extra |
+----+-------------+-------+------+---------------------------------------------------------+--------------+---------+-------------+------+-------------+
| 1 | SIMPLE | n | ref | status,uid,node_status_type,tracker_user,tracker_global | tracker_user | 8 | const,const | 77 | Using where |
+----+-------------+-------+------+---------------------------------------------------------+--------------+---------+-------------+------+-------------+
1 row in set (0.00 sec)

User comments query:
EXPLAIN SELECT n.nid, n.title, n.type, n.changed, n.uid, c.timestamp AS last_updated FROM comments c INNER JOIN node n ON n.nid = c.nid WHERE n.status = 1 AND c.status = 0 AND c.uid = 1 ORDER BY last_updated DESC;
+----+-------------+-------+------+----------------------------------------------------+--------------+---------+-----------------+------+-------------+
| id | select_type | table | type | possible_keys | key | key_len | ref | rows | Extra |
+----+-------------+-------+------+----------------------------------------------------+--------------+---------+-----------------+------+-------------+
| 1 | SIMPLE | c | ref | lid,tracker_user,tracker_global | tracker_user | 5 | const,const | 47 | Using where |
| 1 | SIMPLE | n | ref | PRIMARY,status,node_status_type,nid,tracker_global | nid | 4 | fk_portal.c.nid | 1 | Using where |
+----+-------------+-------+------+----------------------------------------------------+--------------+---------+-----------------+------+-------------+
2 rows in set (0.00 sec)

These are running on my company's portal, but the query plan shouldn't differ elsewhere.