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.