ASCII-visualize a graph
APL (171 166 162 chars, all bonuses: 999 - 171 166 162  + 20 + 20 + 200 = 1068 1073 1077) 

This is the longest golfed APL program I've written so far. This might be slightly cheating, but there's nothing in the question that actually disallows this. What I'm doing is putting all the nodes on a vertical line and drawing the graph as an arc diagram. It is obviously still a graph though.

It still took me a few hours.

V←' '⍴⍨99,⍨2×⍴P←∪,C←(2,⍨2÷⍨⍴G)⍴G←G/⍨⎕A∊⍨G←⍞⋄V[2×⍳⍴P;50]←P⋄M←1⋄G←⍴D←{⍵[⍋⍵]}¨↓P⍳C⋄{V[A B←⍵;L←50+M×⌽⍳G]∘←'-'⋄V[A+⍳B-A;⊃L]∘←'|'⋄V[⍵;⊃L]∘←'+'⋄M×←¯1⋄G-←1}¨2×D[⍒|-/↑D]⋄V


The nodes must be single uppercase letters, so it supports 26 nodes maximum. It can handle crossed lines, and each node can have as many connections as the display will handle.

Example output:

A,B C,A C,D

      +-A--+                                              
      |    |                                              
      +-B  |                                              
           |                                              
        C+-+                                              
         |                                                
        D+   

A,B C,A B,A A,D A,E F,G C,G

          +--A-+-+-+                                           
          |    | | |                                           
          |  B-+ | |                                           
          |      | |                                           
        +-+--C   | |                                           
        |        | |                                           
        |    D---+ |                                           
        |          |                                           
        |    E-----+                                           
        |                                                      
        |   +F                                                 
        |   |                                                  
        +---+G                                                 


 T,H E,Q U,I C,K B,R O,W N,F O,X J,U M,P S,O V,E R,T H,E L,A Z,Y D,O G,S

               +---+----------T                                                 
               |   |                                                            
               |   +-------+--H                                                 
               |           |                                                    
               |           +--E---------+-------+                               
               |                        |       |                               
               |              Q---------+       |                               
               |                                |                               
               |     +--------U---------------+ |                               
               |     |                        | |                               
               |     +--------I               | |                               
               |                              | |                               
               |              C-------+       | |                               
               |                      |       | |                               
               |              K-------+       | |                               
               |                              | |                               
               |       +------B               | |                               
               |       |                      | |                               
               +-------+------R               | |                               
                                              | |                               
             +----------------O-----+-----+-+ | |                               
             |                      |     | | | |                               
             |                W-----+     | | | |                               
             |                            | | | |                               
             |           +----N           | | | |                               
             |           |                | | | |                               
             |           +----F           | | | |                               
             |                            | | | |                               
             |                X-----------+ | | |                               
             |                              | | |                               
             |                J-------------|-+ |                               
             |                              |   |                               
             |                M---+         |   |                               
             |                    |         |   |                               
             |                P---+         |   |                               
             |                              |   |                               
             |   +------------S-------------+   |                               
             |   |                              |                               
             |   |            V-----------------+                               
             |   |                                                              
             |   |            L-+                                               
             |   |              |                                               
             |   |            A-+                                               
             |   |                                                              
             |   |           +Z                                                 
             |   |           |                                                  
             |   |           +Y                                                 
             |   |                                                              
             +---|------------D                                                 
                 |                                                              
                 +------------G