user5093: I got an Ethermega, and learned that Pin 13 already has a LED. 
Are there other digital pins with special circuitry or already allocated to a specific function? (like usb,serial,ethernet,sd, etc)
I need about 30 inputs so I can skip some if that would avoid headaches.

user2881: D4: ChipSelect for the SD card reader (can be used if no SD is present)
D0 and D1 are Serial RX and TX (just like any other arduino)
D10: Ethernet enable line
D13: led. Led is connected via a mosfet, so it doesn't interfer (like on the uno)
D50, D51, D52: SPI for the ethernet chip and SD card
All this was found in the schematic

user89: Don't worry about the led on pin 13, it just sits there but doesn't block anything. 
You can still use the pin as a normal IO pin.
You didn't mention whether your 30 inputs are digital or analog, so let's have a look at digital input first.
I have never used the MCP23017 mentioned by Martynas, but the linked article looks very interesting and I'll definitely order one of these amazing chips!
Another option might be using 8 bit PISO (parallel in - serial out shift registers, such as the 74HC165. Consider this as the complement to the 75HC595 for output. These shift registers are dirt cheap (around 0.3 €), are available as DIP (important for breadboarding) and can be run via SPI. 
Advantages: 

it's fast to read in 8 digital lines into a byte (why would one want to use more than a bit for the state of a digital input?)
the shift registers can be daisychained, subsequent calls of ShiftIn allows to read all (digital) input states into a corresponding data structure (array of bytes, etc.) using just three pins on your Arduino.


5093: <p>I got an Ethermega, and learned that Pin 13 already has a LED. </p>

<p>Are there other digital pins with special circuitry or already allocated to a specific function? (like usb,serial,ethernet,sd, etc)</p>

<p>I need about 30 inputs so I can skip some if that would avoid headaches.</p>
 2881: <p>D4: ChipSelect for the SD card reader (can be used if no SD is present)</p>

<p>D0 and D1 are Serial RX and TX (just like any other arduino)</p>

<p>D10: Ethernet enable line</p>

<p>D13: led. Led is connected via a mosfet, so it doesn't interfer (like on the uno)</p>

<p>D50, D51, D52: SPI for the ethernet chip and SD card</p>

<p>All this was found in the <a href="https://github.com/freetronics/EtherMega/raw/master/EtherMega.pdf" rel="nofollow">schematic</a></p>
 89: <p>Don't worry about the led on pin 13, it just sits there but doesn't block anything. </p>

<p>You can still use the pin as a normal IO pin.</p>

<p>You didn't mention whether your 30 inputs are digital or analog, so let's have a look at digital input first.</p>

<p>I have never used the <strong>MCP23017</strong> mentioned by <em>Martynas</em>, but the linked article looks very interesting and I'll definitely order one of these amazing chips!</p>

<p>Another option might be using 8 bit PISO (<em>parallel in - serial out</em> shift registers, such as the <strong>74HC165</strong>. Consider this as the complement to the 75HC595 for output. These shift registers are dirt cheap (around 0.3 €), are available as DIP (important for breadboarding) and can be run via <a href="http://arduino.cc/en/Reference/SPI" rel="nofollow">SPI</a>. </p>

<p>Advantages: </p>

<ul>
<li><p>it's fast to read in 8 digital lines into a byte (why would one want to use more than a bit for the state of a digital input?)</p></li>
<li><p>the shift registers can be <em>daisychained</em>, subsequent calls of <a href="http://arduino.cc/en/Reference/ShiftIn" rel="nofollow">ShiftIn</a> allows to read all (digital) input states into a corresponding data structure (array of bytes, etc.) using just <strong>three pins</strong> on your Arduino.</p></li>
</ul>
