inp='[Regular expressions] - [rather complex] and "extensive theme".'
out,a,b='',0,0

for i in inp:
  if i=='[':
    a=1
  elif i==']':
    a=0
  elif i=='"':
    b^=1
  elif i==' 'and not(a or b):
    out+='#'
    continue
  out+=i

print inp,'\n',out

$ python test.py
[Regular expressions] - [rather complex] and "extensive theme". 
[Regular expressions]#-#[rather complex]#and#"extensive theme".