In "A Short Victorious War", HMS Hotspur (named for Hornblower's ship in Hornblower and the Hotspur) is destroyed in combat with a Havenite crusier 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The same book had a group of Havenite revolutionaries gathering in a tennis court, back when the series was thick with historical references.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.
The first Havenite revolution is led by a man named "Rob S. Pierre", heading the "Committee of Public Safety". In the French Revolution a committee of the same name was for some time led by...Robespierre.