How important is base size in Warhammer 40K?
It's a grey area, but it's preferred that models be played with the bases provided with them with some exceptions for scenic bases.  Generally as long as you haven't modeled for a clear advantage(such as using a base that's 9" tall) most players will be OK with it.  To be on the safe side, you should have a standard based guy to swap in for the scenic base model it it ever appears your custom base would have an effect on the game. 

There was an issue a few years back at a GW sponsored GT where a Demon player who won the tournament used smaller than standard bases for his Bloodcrushers.  It was felt that this gave his particular army an unfair advantage due to some of that codex's unique rules. As a result, most tournaments will have a policy like this one from the Nova Open:


  Basing Policy
  
  
  Models must be played on the bases provided with them. 
  Models may    be played on scenic bases of identical size to the bases provided    with them.  If  you have a question, ask ahead of
  time. 
  
  If your    scenic bases are smaller than they should be, be aware that you may    be asked not to  use the models at all (if the
  organizers believe you    brought them on such bases to gain an 
  advantage), or to count them    as the appropriate base size. 
  If your scenic bases are larger than    they should be, the above (in re: smaller bases) applies as  well.     Additionally, keep in
  mind that if an opponent is able to reach one    of your larger bases 
  with a shooting attack or charge, you may not    use the excuse of
  base size to prevent it.  The  corollary does NOT    apply – you may
  not gain extra range or charges due to larger bases.     In  short,
  you gain no advantages for unusual base size, but may gain
  additional handicaps. 
  
  Skimmers must be mounted (but not necessarily    glued) on the bases provided with them, save  for situations where    the rules allow for
  / require otherwise.
  
  We recognize that some    skimmer bases are largely impractical for mounting your units on;  if    you have a different basing route
  you've gone with, simply give us a    heads up ahead of  time – we’ll
  work to help ensure the comfortable    play ability and stability of
  your models
  
  


Most players I know will try to conform to the big tournament guidelines. Of course, I play with a fairly competitive group that hits a few big GT's every year.