Mutsu

Mutsu (pop. 65,000) is a fairly grim town of gray concrete and rusting corrugated iron with no attractions to speak of, across the bay from Aomori. However, it serves as the central transport hub of the peninsula, and you're likely to pass through on your way. Hotokegaura, Omazaki, Shiryazaki, Osorezan and Yagen Onsen are all an easy drive away. Mt. Kamafuse overlooks the city and offers a couple chair lifts in the winter and a decent hike in the summer.
Since the amalgamation of Mutsu with three neighboring towns in 2005, most of the peninsula is now within city limits, but this article covers only the town.

Mutsu is well connected by Shimokita standards.

By train

The JR Ominato line from Noheji (on the Tohoku main line) passes through Shimokita station (下北駅) in the southern suburbs of Mutsu.
From Tokyo station it takes roughly five hours to reach Shimokita. You will need to take three trains: The Tohoku Shinkansen Hayate to Hachinohe, the Aoimori Railway to Noheji, then the JR Ominato local to Shimokita station. This trip will make your wallet almost ¥17,000 lighter each way.
The Japan Rail Pass and JR East Rail Pass fully cover the trip, including the segment on the Aoimori Railway between Hachinohe and Noheji. Note that seats on the Hayate bullet train require a seat reservation (free with a Pass).

By bus

Buses from Mutsu's central bus terminal connect to various points in the peninsula, including Ohata (35 min, many daily), Ōma (1½ hr, 8 daily) and Mount Osore (30 min, 4 daily). No direct services to the Yagen Valley though, you'll have to connect through Ohata in time to catch the single daily bus.
There are several services daily to Aomori (3½ hr) and even occasional direct sleeper buses to Tokyo.

Local bus services provide transportation around Mutsu, but the center is small enough to walk.

• The northern command of the Japan Maritime Self-Defense Forces is located on the road to Kawauchi, at the very edge of the city. Visitors can request tours of the base, which is home to several destroyers and other vessels. (These tours are unlikely to be available in English).

• Mt. Kamafuse overlooks the city and offers a couple chair lifts in the winter and a decent hike in the summer.
• There are a few onsen on the outskirts of Mutsu.

Central Mutsu has a number of quaint bars and restaurants.

Mutsu has a wide selection of reasonably cheap lodgings (¥6,000 with two meals), and the tourist information office is glad to help you book.

• B&B MuuA very atmospheric homestay with guest rooms located in the attic section of a log house, owned by an engineer specializing in wooden constructions. The host speaks very limited English, so some basic knowledge of Japanese will come in very handy, but he is otherwise very knowledgeable about the area and friendly. Breakfast costs extra, but tea and coffee are provided for free in the living area downstairs. Reservations can be made via e-mail. The location is given on this Google map. 3900 to 4400 yen/night, depending on the season.

Mutsu Tourist Office (Masakari Plaza, tel. +81 175-22-0909), near the bus terminal, is helpful and can provide basic information in English, not just for Mutsu but the entire peninsula. They will also book accommodation for you.

• Mount Osore (Osorezan) — Japan's gateway to Hell, with boiling technicolor hot springs
• Yagen Valley — low-key hot springs in a near-untouched valley
• Hakodate — From Hakodate ferry arraived at Oma.