What is an alternative to bitwise flags?

Question

I was trying to be smart and elegant, and I ended up shooting myself in the foot by coding my entire application to use flags to store various combinations of settings.
Now, I have hit a point where I have > 64 options. I need to move away from flags or I will be forced to create additional fields, which will make my application really messy given its current state.
What should I consider as an alternative to using flags other than creating a separate boolean variable for each option?
By flags, I mean bitwise flags, e.g.:
[Flags]
public enum Time
None = 0
Flag1 = 1,
Flag2 = 2,
Flag3 = 4,
Flag63 = ...

Answer 1

You could use a BitArray in conjunction with static fields to provide labels for the bits:
static class Flags
public static int WorkProperly = 0;
public static int CompileFaster = 1;
public static int AutoImproveCodeQuality = 2;
class FlagTest
static void Main(string[] args)
BitArray bits = new BitArray(100); // > 64
bits[Flags.AutoImproveCodeQuality] = true;
Or, with an enum, but you'd have to cast the value every time:
enum Flags
Never = 0,
MostOfTheTime,
Sometimes,
OddThursdays,
WhenPigsFly
BitArray bits = new BitArray(1000); // lots of bits
bits[(int)Flags.Sometimes] = true;