Alternating between a PrC and a core class.
Maxing out one PrC and moving on to another.
I don't see either of these as a problem.
Alternating between two unrelated PrCs (a deepwood sniper who is also progressing as a windrider).
Having two or more PrCs with opposing 'flavor text' requirements.
I don't see the first as a problem. Say a player wants to play Zorro. The tough DM wil say, "That's too bad. Zorro's a munchkin." To play a guy like Zorro, you NEED the Duelist and Lasher PrCs, because finesse-based fighters and whip-users are extremely weak in 3E.
To have opposing flavors is a bit different, though. If a player wanted to alternate levels between a brutish, barbarian PrC and a sophisticated, suave PrC, it would just be too strange.
Alternating between two related PrCs (a deepwood sniper who is also advancing in the order of the bow).
There's definite munchkin potential there, but I don't see a justifiable reason to deny it. Combining PrCs in and of itself is not a problem, although certain PrCs are themselves a problem.
Having only 'cheese levels' in one PrC (perhaps to qualify for your main one).
Having 'cheese levels' in two or more PrCs.
I'm okay with the first. Some PrCs have outrageous requirements for certain characters. For example, a Sorcerer who wants to be an Elemental Savant is going to have a heck of a time qualifying because of the extremely high cross-class skill requirements. That's just not right.
But if you've got "cheese" levels in more than 1 PrC, that's really pushing it.
Having three or more PrCs at any level.
For a high-level campaign, this isn't a problem. PrCs are already restrictive in their prerequisites. There's munchkin potential here, of course, but that's usually more due to specific poorly designed PrCs than anything else.