Multiclassing with the Samurai is practically a requirement, because you need some form of bonus damage to make TWF work properly. But because the Samurai’s TWF skills progress so slowly, it’s tricky to pull off.
• Bard: While in theory beneficial for bonus damage through Inspire Courage, the alignment issue is thorny. It can still work, however, through a combination of Paladin and Devoted Performer. Complementary saves. Works best with Eberron, which allows you to swap a song (Inspire Competence, for example) for a feat like Song of the Heart, which improves damage.
• Binder: I didn't think much of this at first but actually it works OK and even has plenty of flavor fit with the Samurai: Replace all the vestiges with long-dead spirits of your ancestors and you're rolling. The Pact Augmentation ability and several vestiges (Andromalius, Eurynome, among others) give bonus damage. And best of all, they boost flexibility -- they let you do things a regular Samurai could never do. Bail out after 4, 5 or 8.
• Cleric: A useful dip for the Turn Undead ability, which can power Divine Might and give you some Charisma synergy. Pick domains that give abilities that aren’t tied to your cleric level, such as War and Fate.
• Dragon Shaman: The aura to boost damage works, though you'd need five levels to get to +2. And the Breath Weapon helps give you a ranged attack.
• Duskblade: I'm still looking at this one. It may have enough spell slots to make Arcane Strike worth it.
• Fighter: This gives you shield proficiency (useful for Improved Buckler Defense) and extra feats, of course. Players Handbook II's Melee Weapon Mastery makes Fighter4/Samurai16 a decent option.
• Knight: Makes some flavor sense and Knight's challenge can boost your damage.
• Hexblade: You get some Charisma synergy from the Curse/Saves, and can use Arcane Strike to help power your damage. Worth looking at as either a dip or 9-level investment (in the latter case, it probably requires Battlecaster and Mithril Full Plate to get full use here.)
• Incarnate: Gives you soulmelds that are source of bonus damage, though you can only be Lawful Neutral with this class.
• Marshal: Good Cha synergy with dips and some bonus damage.
• Monk: You’re obviously burning the Wis to AC with Heavy Armor (and probably Evasion, too) but the feats and saves are nice. Grabbing some of the alternative monk styles would probably be helpful.
• Paladin — Can be very nice if you’re using the Half-Orc Substitution levels, which give morale bonus to damage and an Intimidate-enhancing quality. Even a 2 level dip gets you Cha to Saves.
• Rogue: An obvious source of TWF bonus damage, but Evasion doesn’t work in Heavy Armor.
• Sorceror: Useful in some Gish-type builds, though a TWF style will have some problems with Somatic spells.
• Sohei: Nobody ever takes the Sohei for anything. But it gives Iajutsu Focus as class skill, Ki Frenzy and Weapon Focus, though mixing the two classes may raise flavor issues in some campaigns.
• Soulknife: Soulknives can’t generate a bastard sword & short sword mind blade at the same time, but you could use Katana Mind Blade and a physical Wakazashi, or vice versa, depending on how many Soulknife levels you have. However, the Soulknife’s Short Sword Mind Blade is a true Short Sword (and does piercing, not slashing damage, disrupting the Flay Foe tactic). Complementary saves.
• Wilder: Charisma to Touch AC, and has a handful of augmentable powers that can help a good bit. But you have to choose between ITWF (at Samurai11) and either Schism or Metamorphosis (at Wilder10), which kind of stinks. Gets shield proficiency. Take this for 6 levels (grab expanded knowledge-hustle for full attacks + Improved Staredown) or 9 levels (for maxing out damage with ITWF + Offensive Precognition.
Arcane Duelist: Charisma to AC in armor. Nice. http://www.wizards.com/default.asp?x=dnd/re/20030224a
Disciple of Dispater (BoVD): A great all-around tank/damage-dealer, with bonus damage (keyed to Con.) and Monk-like saves.
Exotic Weapon Master (CW): Normally a no-brainer for Bastard Sword specialists, you actually have to think about it with Samurai because you won’t be using your Katana two-handed very often (unless you use Trick No. 4, above)
Ghost-Faced Killer: Cha synergy and complementary feats. Requires Hide/MS 6, so a dip into Monk, Rogue or other base class is probably required.
Iajutsu Master (OA): While in some ways this makes no sense at all — it’s an unarmored katana specialist, while the CW Samurai is about Heavy Armor. But you almost qualify automatically, and the PrC does value Charisma, so it’s worth mentioning. You’ll need either Human Paragon or Sohei to qualify.
Incandescent Champion (Incarnum): A dynamite class, as it gives you bonuses to damage and intimidate.
Iron Mind (RoS): A psionic class built around the use of heavy armor. You probably won’t have room for much of this, but Samurai11/Wilder2/IronMind7 could be an option.
Knight of the Sacred Seal: Used with Binder, it allows Paladin multiclassing so you have a shot at convincing a DM of this. Cha-based abilities.
Justiciar of Taiia (D&Dgods): Nice in a couple of respects: Sneak Attack, Complementary saves, good skills, bonus Exotic Weapon Proficiency and some spells. Neatest of all is the Combat Insight: +2 to hit/ac offsets the TWF penalties (improves to +4 at level 5)
Kensai (CW): If you don't really care about the two-weapon fighting, it's a very good class. A good bailout option if you're already playing a Samurai (but haven't reached level 11 yet) and you're sick of the TWF thing.
Knight of the Middle Circle: One-level dip gets you +2 to hit/ac combat insight.
Menacing Brute (RoD, Half-Orc): Useful for the intimidation ability, which keeps foes shaken for 1 round/class level.
Mirumoto Niten Master (OA): Only mentioned because of the unusual use of TWF; this PrC uses the short sword for defense, not attack. It’s only worth thinking about if you have a Shugenja in the party, however, due to a number of synergistic abilities.
Raumanthari Battlemage: If you’re going to be using Arcane Strike to boost damage, it’s worth looking at since you’ve got the EWP (Bastard Sword) already. http://www.wizards.com/default.asp?x=dnd/iw/20030413c
Suel Arcanamach: Charisma-based casting in armor, with some nice benefits. Could be a good use of Arcane-Strike boosted damage, though it’d be a lot better if this PrC would work with Raumanthari Battlemage. It doesn’t, because it lacks evocation spells.
Tempest: Sounds like a good idea at first, with the TWF versatility and TWF defense, both of which would help a Samurai quite a bit. But most of the PrC’s features only work in light armor or no armor, and it requires Dex 13 to get into. Yet another failure of synergy — it’s like WotC wrote up the Samurai class and then forgot it ever existed.
War Mind: Great tanking PrC and one that rewards lots of attacks, because Sweeping Strike can make all of them count twice.