If you have a copy of Griffiths, he has a nice discussion of this in the delta function potential section. In summary, if the energy is less than the potential at $-\infty$ and $+\infty$, then it is a bound state, and the spectrum will be discrete:
$$
\Psi\left(x,t\right) = \sum_n c_n \Psi_n\left(x,t\right).
$$
Otherwise (if the energy is greater than the potential at $-\infty$ or $+\infty$), it is a scattering state, and the spectrum will be continuous:
$$
\Psi\left(x,t\right) = \int dk \ c\left(k\right) \Psi_k\left(x,t\right).
$$
For a potential like the infinite square well or harmonic oscillator, the potential goes to $+\infty$ at $\pm \infty$, so there are only bound states.
For a free particle ($V=0$), the energy can never be less than the potential anywhere***, so there are only scattering states.
For the hydrogen atom, $V\left(r\right) = - a / r$ with $a > 0$, so there are bound states for $E < 0$ and scattering states for $E>0$.
Update
*** @Alex asked a couple questions in the comments about why $E>0$ for a free particle, so I thought I'd expand on this point.
If you rearrange the time independent Schrödinger equation as
$$
\psi''= \frac{2m}{\hbar^2} \left(V-E\right) \psi
$$
you see that $\psi''$ and $\psi$ would have the same sign for all $x$ if $E < V_{min}$, and $\psi$ would not be normalizable (can't go to $0$ at $\pm\infty$).
But why do we discount the $E<V_{min}=0$ solutions for this reason, yet keep the $E>0$ solutions, $\psi = e^{ikx}$, when they too aren't normalizable?
The answer is to consider the normalization of the total wave function at $t=0$, using the fact that if a wave function is normalized at $t=0$, it will stay normalized for all time (see argument starting at equation 147 here):
$$
\left<\Psi | \Psi\right> = \int dx \ \Psi^*\left(x,0\right) \Psi\left(x,0\right) = \int dk' \int dk \ c^*\left(k'\right) c\left(k\right) \left[\int dx \ \psi^*_{k'}\left(x\right) \psi_k\left(x\right)\right]
$$
For $E>0$, $\psi_k\left(x\right) = e^{ikx}$ where $k^2 = 2 m E / \hbar^2$, and the $x$ integral in square brackets is $2\pi\delta\left(k-k'\right)$, so
$$
\left<\Psi | \Psi\right> = 2\pi \int dk \ \left|c\left(k\right)\right|^2
$$
which can equal $1$ for a suitable choice of $c\left(k\right)$.
For $E<0$, $\psi_k\left(x\right) = e^{kx}$ where $k^2 = - 2 m E / \hbar^2$, and the $x$ integral in square brackets diverges, so $\left<\Psi | \Psi\right>$ cannot equal $1$.