Farthing: Pagus
Three-farthing stone: Saxum trium pagorum
Bindbale Wood: Fascisarcinae silva
Oatbarton: Avenopraedium
Bywater: Adaquam
The Hill: Collis
Hobbiton: Hobitum
Needlehole: Viaracum
Nobottle: Novaedificium
Rushock Bog: Carculopalus
Overhill: Transcollis
Tookbank: Tuciclivium
Tuckborough: Tucium (I interpret Tuck- as a debased Took)
The Water: Aqua
Waymeet: Compitum
Green-Hill Country: Viridicollium regio
Longbottom: Convallis longis
Pincup: Acocalix? (an attempt to translate it as what it looks like)
Bridgefields: Pontocampus
Brockenbores: Foveae melorum
Budgeford: Bogovadum (Budge- as being a debased Bolger getting latinized in pronunciation)
Deephallow: Demissolucus
Dwaling: Soporificium? (if Dwaling is related to dwale)
Frogmorton: Palustranaeum
Girdley Island: Zonorum Insula (Zono + orum)
Marish: Palus
Overbourn Marshes: Palus Suprafontis
Rushey: Carcorum (with orum = ey, island)
Scary: Scarium (simply a latinized spelling)
Shirebourn: Fons civitatis
Stock: Pecuarium (my assumption)
Stockbrook: Rivus pecuarii
Thistlebrook: Rivus carduum
Whitfurrows: Albisulcorum
Willowbottom: Convallis saligneus
Woodhall: Villa Silvana
Woody End: Finis silvae
Yale: Locus paluster (supposing the German translation as "marsh" is valid)
Newbury: Oppidum Novum
Brandy Hall: Villa verenda
Brandywine: Verendivinum ("Wine to be feared", an attempt to stay close to "Baranduin" in spelling. Mr. Brandybuck would thus turn into Verendicaprus - very hobbitish indeed...)
Buck Hill: Caprae Collis
Bucklebury: Capraeum
Crickhollow: Crectocavum (with a latinized Crick-)
Hay: Vepres
Haysend: Finis veprei
Standelf: Saxifodina
Michel Delving on the White Downs: Fodina Major super Summam Albam
Little Delving: Fodina Minor
Sarn Ford: Sarnovadum