Take a card and write out what happens in each scene in note form, for example, Joe tells Abigail about the party on Saturday night. Abigail is upset and storms out. Then add any other important information about the scene such as Description of pub, first mention of Miranda's name, set up Abigail's important job interview. Find a large space such as the floor or a table (I usually do this on top of my bed, cat willing) and spread the cards out. Now you can 'see' your novel in all its glory.
Things to look for...Are the major scenes evenly distributed? Is there variety between mainly action and mainly reaction scenes ie it's not clumped into lots of action followed by lots of reflection? Are the main plot strands kept going? It's very hard to get a feel for your novel when it's several hundred pages of typescript; this method lets you look at it as a whole at one time. When using index cards for Nice Girls Do I realised that I'd 'lost' Will for a bit and quickly inserted a scene to keep him fresh in Anna's - and the reader's - mind.
The other thing I use index cards for timing. Using a diary I make sure that major events such as public holidays actually turn up when they should do. This can be very useful - I'd got stuck on a bit of A Single to Rome until I realised that the May bank holiday provided a convenient opportunity and worked the timing around it.
I've tried using different coloured cards for different characters or plot strands but it got too complicated for me and now I generally use cheap old white, with coloured ones for scenes that I need to add. I like using index cards so much that I'll do a set several times in the course of writing a novel, and then work from a fresh pile of stacked cards. I think they're wonderful - try them today!