Some ideas:

• Since frequency analysis uses the fact that letters (like 'e') are repeated regularly, you can instead replace 'e' with several different symbols (say, 12 of them), so that each symbol only shows up one percent of the time. If you do this for the highest frequency letters, the cipher is much harder to crack!
  
  
• You can also have entire words replaced by certain symbols, especially ones that come up often and contain high-frequency letters (the words "the" and "and", for example) or you can replace important words (like "midnight" if you message was "attack at midnight"). That way, the frequency analysis is thrown off and some words remain hidden even after most of the cipher is broken.
  
  
• Another option is to insert "nulls" -- symbols that don't stand for anything at all! If you have a wide enough variety of nulls in your cipher, it can be pretty hard to crack!