I'm thinking of three possibilities here:
1. A popup dialog that does *not* prevent the game from playing as normal. Basically, one that always stays on top, but allows gameplay to continue behind it. The user can then resize, move or close this as they like, including (if in windowed mode) moving it outside the boundaries of the NL window itself. Pros: Very easy to implement, very flexible. Cons: May be a bit annoying to the user.
2. Overlaying it over the level area, similar to Cheapo: Pros: Shouldn't interfere too much with gameplay, shouldn't be too annoying, should still be fairly flexible. Shouldn't be too hard to implement, either. Cons: It does still somewhat interfere with viewing the level area, and there is also the question of how well this would perform on very small levels, especially at low zooms.
3. When hints are activated, shrink the level area display slightly and use the extra space to display the hint(s). Pros: Won't interfere with gameplay at all (beyond allowing a little bit less of the level to be viewed at once, and zooming out can remedy this if need be). Cons: May be tricky to support longer hint texts, and will be very tricky to implement.
Displaying things such as the arrows in Cheapo is a seperate matter, which could work with any of the three systems, and probably with most other alternatives that anyone might think of.