Some stories just need Loads and Loads of Characters to preserve their Willing Suspension of Disbelief. In large organizations—such as a Space Navy, fantasy army, alien monitoring agency or old-fashioned corporation—there are bound to be multiple people with specific jobs. Your Five-Man Band will not do anything by themselves, after all. You need analysts, Qs, commanders, scientists and so on, and so forth. During the plot, Main Characters will interact with them a lot and they will do important things main characters can't.
Another situation that justifies Loads and Loads of Characters is when your story spans a huge area and/or time. Having multiple POV characters allows you to show reader/viewer the scale and magnitude of events, and all those POVs needs their Five-Man Bands, Mauve Shirts and so on. Look, for example, at David Weber's Safehold: when conflict is local, the number of POV characters is reasonably small, yet when global war breaks out, it multiplies. This brings across the point of global, important conflict that will have its impact everywhere. Likewise, The Wheel of Time starts out relatively small—the starting party is a Power Trio of male Main Characters, a Tomboy and Girly Girl duo, and three mentors in the form of Sword and Sorcerer duo and a Quirky Bard—but quickly starts Going Cosmic when it becomes clear that one of those mains is The Chosen One who will lead the fight against evil. By the second book, the Amyrlin Seat—the president of the series' Witch Species, and the single most powerful person on the continent—is involved, and it only expands from there.
If one of the above occurs and your cast has more characters than katakana, there are a few rules to follow:
- The "Cast of Snowflakes" trope is your friend. It helps your viewers recognize characters. Instead of three white blond girls, have one with short pixie hair and alabaster skin, one older Dark-Skinned Blonde and one with a huge scar on her cheek. This is especially important in visual mediums, where names are used very rarely, but book readers will also remember characters better if you give them memorable visual attributes. Who do you think your readers will recognize amongst a 200-person cast? Alice Smith, or Alice With A Huge Scar?
- Mind that this isn't only about body features. Fearless warrior Charles may be recognized by his silver-blue legendary sword, while cool high school student Bob wouldn't be seen dead without his Cool Shades. All details make difference, just don't make them too small. For example: blond white girl has a butterfly tattoo on her neck and another blond white girl has spider tattoo on her neck. But it's not like camera shows their necks in close detail very often, so they're hard to distinguish.
- One Steve Limit is also a helpful tool, especially in the works where you invent names. Your hypothetical three blond girls shouldn't be called Ann, Annabeth and Anette, or Shia, Shya and Shiiah. It worked in Ed, Edd n Eddy, but this had less that twenty named characters and each of them was different visually. Instead, let's look at Safehold again. Weber was often criticized because in his large cast of My Nayme Is people he broke One Steve Limit rule repetitively, both in titles (Baron Green Hill, Baron Green Valley) and names (Zahn, Zhan, Zhohn, Zhonn and so on), which confused the hell out of readers. Avoid it.
- If your writing contemporary setting or sci-fi, remember that you don't have to use only English names. Britain has population of English, Africans, Arabs, Hindus and various minorities (German, East-European, Polish). Many Europeans work in Arabic countries. America is an absolute mix of nations and races. It goes Up to Eleven in sci-fi settings, where we can expect nations to mix even more. Today Beifu Polański would raise some eyebrows. In 3000 A.D., he'd not.
- Of course, One Steve Limit can be broken. This is especially true if your setting is aiming for realism (after all, almost everyone in real life has people that share their name — some more than others). If you do, you might want to do it as a Plot Point. A creepy orphanage is even creepier when all the inhabitants are little blond girls named Anna. The same Safehold has two characters called Clyntahn, one of whom is often bullied because the other is a complete bastard. Additionally, if you're going to break it, try having one of the characters go by a nickname to distinguish between other characters (for example, the aforementioned Ed, Edd n Eddy had Edd go by "Double D" to distinguish between him and Ed). Tropes Are Tools, but use them with care.
- The larger your cast, the more each character has to differ them from one another. Even if you have two girls that look the same and are called Annie and Anna, turning them into Red Oni, Blue Oni can save the day. The less a person features in the book, the flatter their character can be. Create various One Scene Wonders, Large Hams and similar. Give them quirks, hobbies and twitches. Make Red Oni Annie eat ice-cream all the time and scream cheerfully most sentences, while Blue Oni Anna spends her free time with books and listens to Classical Music. Of course, it goes both ways. The more person features in the book, the more character traits should s/he have. Otherwise your Main Characters are also Flat Characters, a mistake that is rarely recoverable.
- This is another way to safely avert the One Steve Limit. A Song of Ice and Fire has a king, Robert Baratheon, whose two best friends both named their sons after him. However, His Grace is an Adipose Rex Boisterous Bruiser, Robb Stark The Wise Prince driven by Honor Before Reason, and little Robert Arryn a Creepy Child happily snuggling up to My Beloved Smother. For additional ease of differentiation, all three of them are involved in different plot threads, there's only two scenes in the entire series where any of them appear together, and only one of them is even a main character. George R. R. Martin is highly respected for his abilities with Character Development, so Don't Try This at Home, but the point is that it can be done.
- Group characters in your work into Cast Herds. Let's say that you have POVs on both sides of the conflict. Turn them into Five-Man Bands with corresponding functions. Don't make your characters travel alone in twenty different directions. Make them travel in four directions in groups of five and allow relations in group to be similar in each group (Geodesic Cast page picture explains it rather well). Give each of your groups something that differs them from other groups: for example, people from Clan Blond may be the only ones in the setting with blond hair, or Space Republicans might give their spaceships prefix RSS while Space Empire puts SES. These are the details your readers/viewers can use to distinguish one herd from another. Then inside one herd you can (partially) recycle character concepts from another herd.
- Give your reader/viewer clues as to whose POV/scene is this. Observe the difference between these two sentences:
Anna Smith walked slowly through ship's main corridor.Captain Smith walked slowly through the main corridor of her RSFS Hurricane.
- If these are opening sentences of chapters in sci-fi with giant space battles, the first sentence tells you only that there's some Anna Smith (which one?) that's aboard a ship (which one?). The second, on the other hand, specifies that you mean Captain Smith (specific person) of the Hurricane (specific ship), which flies the colors of the Republican Space Fleet (specific nation). That should be enough for your readers to understand who are they reading about now.
- If your cast list is huge, include it in your work. Of course, this won't work for the movies, but it's easier for book reader to check the list in the back of his copy than try to remember which Anna Smith are you talking about. For other media, put the list online so that reader/viewer can check it - pageviews on IMDb and The Other Wiki always go up as a showing lets out.
- If all else fails, feel free to hang a lampshade. Acknowledge the fact that your characters cannot be distinguished by having other characters point it out and ask which one is which. But still differ the indistinguishable characters, so that Bob (and reader/viewer) can ask something along the lines: Are you Annie the Ice-Cream Eater or Serious Anna?
If you can't recognize characters in your own work, you're doing it wrong. You're the author; you have more investment and care in these characters than does anyone else. The Reader will never put more effort into your story than you will (and nor should they). So if these characters aren't unique to you, there's absolutely no hope they'll be unique to anyone else.