Ascii art equation visualizer
Python 2, 1666 chars

The layout is actually pretty easy - it's the parsing of the input that's a royal pain.  I'm still not sure it is completely correct.

import re,shlex
s=' '
R=range

# Tokenize.  The regex is because shlex doesn't treat 3x and x3 as two separate tokens.  The regex jams a space in between.                                                 
r=r'\1 \2'
f=re.sub
x=shlex.shlex(f('([^\d])(\d)',r,f('(\d)([^\d])',r,raw_input())))
T=[s]
while T[-1]:T+=[x.get_token()]
T[-1]=s

# convert implicit * to explicit *                                                                                                                                          
i=1
while T[i:]:
 if(T[i-1].isalnum()or T[i-1]in')]')and(T[i].isalnum()or T[i]in'('):T=T[:i]+['*']+T[i:]
 i+=1

# detect unary -, replace with !                                                                                                                                            
for i in R(len(T)):
 if T[i]=='-'and T[i-1]in'=+-*/^![( ':T[i]='!'
print T

# parse expression: returns tuple of op and args (if any)                                                                                                                   
B={'=':1,',':2,'+':3,'-':3,'*':4,'/':4,'^':5}
def P(t):
 d,m=0,9
 for i in R(len(t)):
  c=t[i];d+=c in'([';d-=c in')]'
  if d==0and c in B and(B[c]&lt;m or m==B[c]and'^'!=c):m=B[c];r=(c,P(t[:i]),P(t[i+1:]))
 if m&lt;9:return r
 if'!'==t[0]:return('!',P(t[1:]))
 if'('==t[0]:return P(t[1:-1])
 if'I'==t[0][0]:return('I',P(t[2:-1]))
 return(t[0],)

# parenthesize a layout                                                                                                                                                     
def S(x):
 A,a,b,c=x
 if b&gt;1:A=['/'+A[0]+'\\']+['|'+A[i]+'|'for i in R(1,b-1)]+['\\'+A[-1]+'/']
 else:A=['('+A[0]+')']
 return[A,a+2,b,c]

# layout a parsed expression.  Returns array of strings (one for each line), width, height, centerline                                                                      
def L(z):
 p,g=z[0],map(L,z[1:])
 if p=='*':
  if z[1][0]in'+-':g[0]=S(g[0])
  if z[2][0]in'+-':g[1]=S(g[1])
 if p=='^'and z[1][0]in'+-*/^!':g[0]=S(g[0])
 if g:(A,a,b,c)=g[0]
 if g[1:]:(D,d,e,f)=g[1]
 if p in'-+*=,':
  C=max(c,f);E=max(b-c,e-f);F=C+E;U=[s+s+s]*F;U[C]=s+p+s;V=3
  if p in'*,':U=[s]*F;V=1
  return([x+u+y for x,u,y in zip((C-c)*[s*a]+A+(E-b+c)*[s*a],U,(C-f)*[s*d]+D+(E-e+f)*[s*d])],a+d+V,F,C)
 if'^'==p:return([s*a+x for x in D]+[x+s*d for x in A],a+d,b+e,c+e)
 if'/'==p:w=max(a,d);return([(w-a+1)/2*s+x+(w-a)/2*s for x in A]+['-'*w]+[(w-d+1)/2*s+x+(w-d)/2*s for x in D],w,b+e+1,b)
 if'!'==p:return([' -  '[i==c::2]+A[i]for i in R(b)],a+2,b,c)
 if'I'==p:h=max(3,b);A=(h-b)/2*[s*a]+A+(h-b+1)/2*[s*a];return(['  \\/|/\\  '[(i&gt;0)+(i==h-1)::3]+A[i]for i in R(h)],a+3,h,h/2)
 return([p],len(p),1,0)

print'\n'.join(L(P(T[1:-1]))[0])


For the big input in the question, I get:

 /\         2                     2 
 |     - m x  b          2 + b m x  
 |     --------    = - -------------
 |  3      2                    2   
\/ x  e         dx         b m x    
                           ------   
                        2     2    2
                       b  e       m 


Here's some more tricky test cases:

I:(2^3)^4
O:    4
  / 3\ 
  \2 / 

I:(2(3+4)5)^6
O:             6
  (2 (3 + 4) 5) 

I:x Integral[x^2,dx] y
O:   /\ 2     
  x  | x  dx y
    \/        

I:(-x)^y
O:     y
  (- x) 

I:-x^y
O:     y
  (- x)


That last one is wrong, some precedence error in the parser.