In "A Short Victorious War", HMS Hotspur (named for Hornblower's ship in Hornblower and the Hotspur) is destroyed in combat with a Havenite cruiser squadron. The same book had a group of Havenite revolutionaries gathering in a tennis court, back when the series was thick with historical references.
In "A Whiff of Grapeshot," (the title itself a historical Shout-Out to Napoleon Bonaparte) to Citizen Admiral Esther McQueen finds herself trapped in a crashed vehicle dangling over a lethal drop. She calmly states "Here's my plan" then laughs and explains that it is a classical reference.
In The Shadow of Saganami, while using a "borrowed" freighter to reconnoiter a potentially unfriendly star system, Commander FitzGerald identifies himself as "Captain Teach" and a subordinate as "Lieutenant Kidd".
The children's book David and the Phoenix, prominently featured in At All Costs, is a real book and one of author David Weber's favorites.
A recursive shout-out: Baen Designated Victim Joe Buckley is mentioned in Mission of Honor, as is a starship, Dahak, named for the website that the real-life Buckley runs — which was itself named for a starship from David Weber's own Empire from the Ashes series.
In War of Honor, Zahn's husband Tim is said to be highly regarded by a Manticoran officer named Commodore Tharwan.
Officers named Horn and Stackpole were serving aboard HMS Ajax at the Battle of Solon.
In A Beautiful Friendship, the Harringtons have a meeting at a restaurant called "The Red Letter", owned by a person by the name of Eric Flint, with whom Weber has co-written books in this and the 1632 series. The restaurant and its owner/cook also have a minor presence in the sequel, Fire Season.
A former politician and political commentator in the novella I Will Build My House of Steel is named HillaryPalin.
Lois is the only habitable planet in the Clarke system.
In Flag In Exile, a ChiefO'Brien is mentioned when Honor compares the religious diversity of a Manticoran superdreadnought to a Grayson one. For bonus points, he is described as a Shinto priest and the character who he is presumably a reference to has a Japanese wife.
In Honor Among Enemies, Manticore System Command briefly considers the possibility of assigning the cruiser Amaterasu for escort duty. (It's not available soon enough, though, so another ship is sent instead.)