Python 3, 421 414 410 404 388 395 401 bytes

Golfed:

import sys,re
v,i,c,g,L={},0,[re.sub('( ?)[^9]+','\\1',l).rstrip().split(' ')for l in open(sys.argv[1])],lambda i:v.get(i,int(i)//9),len
while-1<i<L(c):
 d=c[i];l=L(d);e,*f=d;i+=1
 if l>1:
  x,*y=f
  if e:w=list(map(g,f));v[e]=sum(w[::2])-sum(w[1::2])
  elif l==2:j=input();v[x]=int(j)if L(x)%2 else ord(j)
  elif~-any(g(j)for j in y):i=g(x)*9
 elif e:w=g(e);print(w if L(e)%2 else chr(w%128),end='')

Ungolfed:

import sys, re

# Intialise variable table.
vars_ = {}
get_var = lambda i: vars_.get(i, int(i)//9)

# Parse commands.
commands=[re.sub('( ?)[^9]+','\\1',l).rstrip().split(' ') for l in open(sys.argv[1])]

# Run until the current instruction index is out of bounds.
index=0
while 0 <= index < len(commands):
    # Get the current command and increment the index.
    command = commands[index]
    l = len(command)
    first = command[0]
    index += 1

    if l > 1:
        # Handle the "assignment" command.
        if first:
            operands = [get_var(i) for i in command[1:]]
            vars_[first] = sum(operands[0::2]) - sum(operands[1::2])
        # Handle the "input" command.
        elif l==2:
            inp = input()
            vars_[command[1]] = int(inp) if len(command[1]) % 2 else ord(inp)
        # Handle the "goto" command.
        elif not any(get_var(i) for i in command[2:]):
            index = get_var(command[1]) * 9
    # Handle the "output" command.
    elif first:
        val = get_var(first)
        print(val if len(first) % 2 else chr(val % 128),end='')

Pretty much just a literal implementation of the spec, golfed down as far as I can get it.

Run from the command line by supplying a 99 source-code file as the sole argument (e.g. the last example from the OP):

> python3 ninetynine.py countdown.txt
G11G10G9G8G7G6G5G4G3G2G1G
>

As an added bonus, here's a (rather poor) implementation of "99 bottles" in 99: http://pastebin.com/nczmzkFs