Infected batch?
 

Just took off the lid of my Fermenter to take a gravity reading and noticed a very citrusy/funky smell to the beer. This is only my third batch, but I haven't noticed this before. Is it infected? Or can you only tell when you sample it?

Have you tried the search function yet? There are no less than hundreds of threads exactly like this that will answer your questions.

http://www.homebrewtalk.com/f39/think-you-ruined-your-beer-set-your-fears-aside-74520/

go there. it is very very helpful. Also, there is a thread with a whole bunch of photos of peoples infections. I can't find the link at the moment, but if you use the search function I'm sure it will come up.

most of the infections look like congealed milk or mold. I'm sure your beer is fine. Give it some time. The smells could be sulfer or another biproduct of fermentation. I've only brewed 2 batches, but in my time on these forums I've learned one thing.
Relax. Don't Worry. Have a homebrew. If you don't have any yet, have a craft brew.

Never Assume i your beer is infected! It can smell, look and even taste funky at bottling time, but it can change a lot in the bottle or keg...

I second this statement. My orange ale smelled funky at bottle but taste great and smelled great after bottling and kegging.

The beer will put off some pretty funky smells in the fermentor; I believe the term "Rhino Farts" have been use from time to time.
Usually mine has a nice nostril stinging sulfur smell. Lets you know you have beer in the house :D

The smell described by the OP is the smell of krausen. The "nostril burning" smell is actually concentrated CO2. Carbonic acid is what burns.

Great. I assume that the "rhino farts" won't follow the beer into the secondary/keg? lol

As long as you don't siphon the rhinos over. ;)