Lori Brown provides a good tip:
Have you ever had transactional replication mysteriously start showing significant latency at a subscriber server? If so, check to see if the primary keys from the publisher database are missing on the subscriber database!
Replication was showing long latency while the publisher and subscriber servers were not heavily utilized. Microsoft generated stored procedures that are used to send INSERT, UPDATE and DELETE operations from the publisher database to the subscriber database had no indexes to help query performance to the subscriber tables. Since there were no indexes that matched the keys of the statements pushing through data changes, tables were being fully scanned and replication statements were piling up. In other words, the subscriber was missing indexes.
Read on to see how you can check this and also how you can quickly script those missing indexes.