When my fixie is done, it will be my wet weather bike. I'm curious what do you guys do to prevent wet shoes and socks. I've seen shoe covers but they don't seem like they would fit in toe clips. Any suggestions? What do you do?

Fixed gear rain riding.
Rain Pants
Rain jacket
Bagged up shoes
IE:

First line defense: fenders with DIY mudflaps for added coverage.
Second line defense: GoreTex socks or shoe covers. Also, wool socks are really good because they keep you warm even when they're wet, so you stay warm and wet instead of cold and miserable.
Third line defense: (I'm looking into this but haven't done it yet) Adding waterproofing compound to your leather shoes. Better than nothing I'd hope.

And, if you live in an area like Oregon where once the winter rain starts, it doesn't really stop until around April or May, it'd be a good investment to get one of those shoe dryers that gets your shoes dry in an hour or two so you don't have to put wet shoes back on.

You need to buy a good "bootie"
https://www.performancebike.com/shop/...estore_ID=1919

I have some neoprene paddling socks, which don't stay dry. So I bought these instead on several T.O. riders suggestions. $30 from MEC, with rain pants over the tops of the covers my feet stay dry and warm. Easy yot get on and off as well.

my experience with goretex socks is they perform about as well as plastic bags in your shoes...When I would pull them off after riding, I'd pour out half a cup of dirty sweat from them so my feet weren't really staying dry...Plus, your shoes still end up getting soaked from the rain...
I have a pair of the MEC shoe covers (i hate saying "bootie") pictured above and they work well with clipless pedals but not so well with clips and straps...Sugoi makes a shoe cover that works a bit better with clips but I don't know how durable they would be longterm...

I find in ultimate heavy downpours all shoe covers I've tried have a failure point where your feet just get soaked. My MECs give up completely after about an hour and a half, which is really not too bad. So, on really long rides in the winter I wear two layers of booties, the MECS on top and some lighter, lower profile roadie booties underneath. This is good for a bit longer, although nothing's perfect.

I ride clipless btw, you toeclippers might look in to rubber overshoes and powergrips for really cold winter rain. Whatever you get you'd just want to make sure it can take the added wear over the arch.

The Mec ones I bought more for keeping the slushy winter road goo off my feet as much as the rain.

Something else I just thought of: having enough room for circulation in your toes is fundamental. Shoes that are nice and snug are fine for summer but in the cold winter wet they can make your feet feel like a couple of popsicles. On the flip side, your toes will have a fighting chance of staying warm in the wet if there is a generous amount of room in the shoe. I would add this to tarckatina's list as a fourth line of defense.

Shows Pass is revamping their entire line, and they will be releasing two different waterproof booties. Unfortunately, as has been mentioned, these probably won't work well with clips and straps.

I have commuted through Portland OR winters for the last two years and I used a pair of high top gor-tex shoes, lovely. My only complaint was that they are not very breathable.

There are few shoes that keep the water out. But, there are totally impermable socks that work just great.. YOu can walk on water and nothing gets in..

Waterproof hiking boots.
Still fit in my cages, just have to loosen straps a tad. I also use gore-tex gaiters.

maybe some one said this but the best thing ive found so far is putting a plastic grocery bags over my sneakers. i tie the handles together in a loose knot around my ankles and put my leggings over the tops, if im wearing them. you look like a complete idiot but it works. i rode about 30 miles through the berkshires like that and i often ride like that to school, 10 miles. normally my shoes would be soaked within two miles, but throw those bags over and 10 miles later im 95% dry. the only drawback, besides looking stupid, is that the bag can rip easily with some pedal and clip setups. my setup happens to not rip for miles and miles (soma hellyer pedals and soma double cages), by buddies set up rips a bit after like 5 miles (probably the exposed chainring teeth, its a road bike). but yeah two plastic bags, 30 minutes of looking like a dork, and im dry all day long.

This is why you should invest in another pair of shoes for winter.

Cold rain (fall/winter/spring) I wear my 8" boots with platforms.
Warm rain (summer) I wear sandals.

thanks for all the suggestion, but a few clicks into looking at gortex, i found something that i love!
https://www.gore-tex.com/remote/Satel.../1220658751109

it gives me the waterproof shell, yet still allows me to clip into toeclip/strap and doesn't make me look like a nerd (no offense to those with heavier rain condition requiring boots)

I was on the grocery bag program for a while and it works very well. However, I switched from grocery bags to the plastic sleeves that fruit and vegetables go in when you purchase them from a grocery store and I use rubber bands to keep them snug against my shoe and either tuck them into my socks or use leg straps to hold them up. I've found the bags to be pretty much one use only though, so I carry two or more pairs if it's going to be raining all day and I'll be making multiple trips on the bike. Of course, you're still going to look pretty goofy but your feet will be dry.
I've had people give me "props" for taking the precautions to keep my feet dry. Funniest encounter was outside the grocery store when a guy pulled up in a beat-up truck to get a newspaper from the stand next to the bike rack where I was locking up. Upon seeing my system he remarked "Now that's thinking buddy..." to which I replied "Yup....gotta keep my feet dry". He responded with "Hell yeah... it's like Lieutenant Dan said in Forest Gump..." and he proceeds to imitate Lieutenant Dan's quotes about foot hygiene. Then he offers his own advice that "If your feet get wet, you'll get the fungus. If you get the fungus, you'll get the corns. And if you get the corns...then you can't go backpacking EVERY WEEKEND". As an avid backpacker I couldn't help but laugh and smile and say "Amen to that". He offered me a ride but I still had to get my groceries so I had to decline, but it definitely made my rainy, cold day a little brighter and a lot funnier.

Plastic bags over your shoes work as well as any shoe cover in the world. They just wear out quicker. But if you ever buy anything the bags are free. It's easy to keep "inventory". Sandwich bags over your socks under the shoes work incredibly well for dry but cold.
One bag over the sock and one over the shoe is even better for cold. Or cold and wet.