I\'m trying to write a parser in Java for a simple language similar to Latex, i.e. it contains lots of unstructured text with a couple of \\commands[with]{some}{parameters}
You can define a grammar to accept the Latex input, using just characters as tokens in the worst cast. JavaCC should be just fine for this purpose.
The good thing about a grammar and a parser generator is that it can parse things that FSAs have trouble with, especially nested structures.
A first cut at your grammar could be (I'm not sure this is valid JavaCC, but it is reasonable EBNF):
Latex = item* ;
item = command | rawtext ;
command = command arguments ;
command = '\' letter ( letter | digit )* ; -- might pick this up as lexeme
letter = 'a' | 'b' | ... | 'z' ;
digit= '0' | ... | '9' ;
arguments = epsilon | '{' item* '}' ;
rawtext = ( letter | digit | whitespace | punctuationminusbackslash )+ ; -- might pick this up as lexeme
whitespace = ' ' | '\t' | '\n' | '\:0D' ;
punctuationminusbackslash = '!' | ... | '^' ;