Regex!
The main problem here will be that you've got syntax-based rules in case of the nested expressions, i.e. when you're matching \comandnameE{ ... } you don't want to match until the first }, but after the parenthesis balance is even again. I don't know how to take care of that using only Regex. Anyway,
(* Your string condensed into one line *)
tex = "\\commandnameA{Bob}\nblabla\n\n\n\n \\commandnameB{It wasn't Bob}\n\n \\commandnameC{2012}\n\nbla\n\n \\commandnameD{$\\frac{1}{3}$}\n\n \\commandnameE{\\commandnameF{It was Bob!}}\n\n \\commandnamefilename{29}";
(* Regex that matches the inside of a parenthesis of
a `commandname` instruction *)
regex = RegularExpression["\\\\commandname[a-zA-Z]+\{(.+)\}"];
(* Apply regex *)
StringCases[tex, regex -> "$1", Overlaps -> True]
List[
Bob,
It wasn't Bob,
2012,
$\frac{1}{3}$,
\commandnameF{It was Bob!},
It was Bob!},
29
]
Note the trailing } in the It was Bob!} line, which you may have to take care of manually.
The regex is replaced by $1, which is the first matched sub-pattern, i.e. the first parenthesis expression in the regex. $0 would have been the entire expression, i.e. the resulting list would contain all the \commandnameX, the curly braces and so on.
The Overlaps parameter lets the regex match single characters multiple times, i.e. after matching commandE, the already matched character sequence is searched again, yielding the contents of commandF.
If you want to incorporate a dictionary of possible \commandX, simply replace the command in the regex by (command1|foo|bar|command12|...).
\commandnameAetc. to write into some file which you then can read into Mathematica. – celtschk Apr 29 '12 at 19:19commandnameAetc. to write their content into a special file (in addition to what they normally do). That way you'd even get the information if someone invoked them indirectly, e.g. using\let\cnA=\commandnameAand then later\cnA{Bob}. However, if the macros always appear literally, that would be overkill. Anyway, the process of writing to a file from LaTeX is described in http://stackoverflow.com/q/2115379/1032073 – celtschk Apr 29 '12 at 20:04