A wide variety of multiverse-travelling ships have featured in the AH.com The Series. This is a partial list.
All of these tout the acronym prefix 'MES'. We know that three of these - the AH.com, CF.net and AV.net - were built by the Neanderthal Multiverse Empire, then captured by the Human Unity and turned against the Devourer of Worlds. Other ships described as looking similar, also called MES, and with similar website-like names have also featured. These may also be Neanderthal-built ships, perhaps captured and rebuilt by other human powers than the Unity in different timelines.
A wide variety of other shift-capable ships have featured.
Orbital habitats, spacebases and other entities which may or may not be classed as ships.
As is traditional in shows of this type, the AH.com Ship appears to have a virtually endless supply of shuttles, often getting destroyed in every episode. The naming scheme, largely determined by Doctor What, features the name of his cat, random pop culture references and the names of female porn stars.
In Order of Appearance
Alpha - BROKE DOWN AGAIN
Mynx I - Fitted with a shift drive. LIFE, EVERYTHING, AND THE PUB IN THE HUB ; AMERICAN EMPIRE THE HOLDER CANNOT SCENT (in which the Mynx I was destroyed when it was shot down by Confederate fighters and crashed on TL-191, but was replaced by other shift-capable shuttles, also named Mynx).
Mynx VI - CITATION NEEDED ; MONTANA HOWERY AND THE MANTLE OF N00B (abandoned on the Damned Kazakh Border timeline, but apparently retrieved later) ; THE ULTIMATE SHOWDOWN (destroyed by the ASB Batship)
Mynx VII - THE NARCISSUS SYNDROME (apparently abandoned, left docked to Mirror AH.com Ship)
“Wash Me” - IN THE LAND OF THE BLIND
Long John Baldry - AH.COM THE SORTA-KINDA-MAYBE NEXT GENERATION
Jenna Jameson - IT CAME FROM HOLLYWOOD
Buckaroo Banzai - IT CAME FROM HOLLYWOOD
Muad'Dib - AVE, B'HARNY
C.C. Rider - THE RETURN OF THE KING
Baron Munchhausen - DINOS & NAZIS & DEROS, OH MY!
Sibyl - HARBINGERS
Mímir - HARBINGERS
Mimi Miyagi - A SMALL PROBLEM
Jessica Alba - HAIR TODAY GOTTERDAMMERUNG TOMORROW
Jennifer Garner - HAIR TODAY GOTTERDAMMERUNG TOMORROW
Halle Berry - HAIR TODAY GOTTERDAMMERUNG TOMORROW
Daisy Chain - CITATION NEEDED (fell into chasm on WikiWorld)
S&M - UNRESOLVED ISSUES
Piri Reis - CASINO IMPERIALE