Chickens

Egg-laying hens

An estimated 95% of all eggs in the United States are produced in conventional cage systems, sometimes called battery cages. [They] typically provide each laying hen an average of 67 square inches of floor space. In some egg operations, hens have less space.

Source: Table Egg Production and Hen Welfare: Agreement and Legislative Proposals - 2014

Statistics for many other countries can be found in: Statistics: Laying Hens - Compassion in World Farming - 2013. There's too much data to paste here. The percentages range all the way from 0 to 100.

From the same report:

Between 87% and 100% of laying hens producing eggs for all except one of the supermarkets surveyed are beak-trimmed. Only Waitrose reported a much lower proportion (36%) of hens being beak-trimmed. Overall, probably at least 90% of laying hens in the UK are beak-trimmed

Induced molting usually involves removal of feed for periods of 5 to 14 days followed by a low nutrient ration for the remaining days in a 28 day molt program. [...] Molting programs involve an estimated 75-80% of the commercial flocks in the US.

Source: Proceedings of the 50th Western Poultry Disease Conference - 2001

Broiler (meat) chickens

Studies consistently show that approximately 26-30% of broiler chickens suffer from gait defects severe enough to impair walking ability, and additional research strongly suggests that birds at this level of lameness are in pain.

Source: An HSUS Report: The Welfare of Animals in the Meat, Egg, and Dairy Industries. 5 references are cited for this sentence. From one of those references:

We assessed the walking ability of 51,000 birds, representing 4.8 million birds within 176 flocks. [...] over 27.6% of birds in our study showed poor locomotion and 3.3% were almost unable to walk. [This is] despite culling policies designed to remove severely lame birds from flocks.

Therefore it's safe to regard these numbers as typical.

In 2011, 15,951 commercial operations raised broilers for meat in the 17 sample States

A table then shows that these farms produced 8,060,557,235 broilers in 2011, an average of over 500,000 chickens per operation.

Source: Technology, Organization, and Financial Performance in U.S. Broiler Production (USDA) - 2014

Cows

From the Executive Summary of the 2007 National Market Cow and Bull Beef Quality Audit about cows (whether raised for beef or dairy) being brought to slaughter:

83% of all plants used electric prods for moving cattle to the restrainer. 65% used electric cattle prods on more than 25% of their cattle. [...] 39% of plants audited showed the aggressive use of [other] driving aids when moving cattle to the restrainer.

49% of dairy cows showed some level of lameness in holding pens (see graph on page 7).

Steers weighing 500 pounds and over totaled 16.4 million head, up slightly from one year ago. Bulls weighing 500 pounds and over totaled 2.23 million head

Since steers are castrated and bulls are not, 88% of male cows are castrated.

Source: USDA cattle inventory - 2017

Furthermore, pain relief isn't used 70 - 80% of the time:

Respondents reported not providing analgesic drugs to approximately 70% of calves castrated at < 6 months of age.

Source: Analgesic drug administration and attitudes about analgesia in cattle among bovine practitioners in the United States - 2011

One in five practitioners report using an analgesic or local anesthetic at the time of castration.

Source: A survey of castration methods and associated livestock management practices performed by bovine veterinarians in the United States - 2009

Dairy cows

approximately 88% of Norwegian dairy cattle, 75% of all Swedish dairy herds and more than one third of German dairy cows are kept in tie-stall housing systems, often without pasturing. According to the 2007 USDA report 62% of US dairy farms had tie-stall barns. In Romania, the tied system is used in approximately 75% of the middle sized and large farms and in 90% of the small farms

Source: Dairy cows welfare quality in tie-stall housing system with or without access to exercise

(this means that the cow is "held by a neck chain, strap, or stanchion such that she can lie down but cannot turn around")

From Heifer Calf Health and Management Practices on U.S. Dairy Operations, 2007:

Overall, 94.0 percent of operations routinely dehorned heifer calves while they were on the operation during the previous 12 months. A lower percentage of large operations (64.3 percent) dehorned heifer calves than small or medium operations (97.3 and 92.6 percent, respectively). [...] For operations that routinely dehorned heifer calves during the previous 12 months, more than two-thirds (69.1 percent) used a hot iron [...] For operations that used a hot iron to dehorn calves, 13.8 percent used analgesics/anesthetics when dehorning calves.

Tail docking is currently prohibited in California and must not be performed as a routine management procedure in the European Union. [...] About half of operations [in the U.S.] (51.4 percent) had no cows with the tail docked. [...] On about one of seven operations (14.6 percent), all cows had the tail docked. [...] Overall, about 4 of 10 cows (38.8 percent) had the tail docked. [...] The majority of operations with tail-docked cows (90.3 percent) did not routinely use analgesics or anesthetics for tail docking, compared with 1.1 percent that routinely used analgesics or anesthetics. Operations that routinely used analgesics or anesthetics represented 0.9 percent of cows with the tail docked.

About one-half of operations (50.3 percent) routinely removed extra teats from heifer calves [...] One of 10 operations (10.6 percent) routinely used analgesia or anesthesia during extra teat removal

94.9% of operations observed at least one case of clinical mastitis, a painful, inflammatory infection of the udder caused by milking. 16.5% of cows had mastitis in 2006, as identified by producers.

Source: Dairy 2007, Part I: Reference of Dairy Cattle Health and Management Practices in the United States

Surveys on mastitis in Nordic countries in 1997 found:

18.3 cases per 100 completed or terminated lactations in Sweden to 25.8 per 100 cow-years in Norway

Source: Cumulative Risk of Bovine Mastitis Treatments in Denmark, Finland, Norway and Sweden

Pigs

By far the most common system in use is the farrowing crate, with an estimated 85% of all sows in the U.S. being housed in this type of system at farrowing.

Source: Swine Welfare Fact Sheet (USDA) - 2011

(a farrowing crate is a metal enclosure only slightly bigger than the sow that she spends 4-5 weeks in around the time of giving birth)

One in every four sows (26 per cent) is bred outdoors in the UK, but just one in twenty pigs (5 per cent) spend the growing period outdoors and one in a hundred are finished on free range.

56 per cent of UK sows farrow in some form of farrowing crate

Source: Structure of the UK Pig Industry

only 17.3 percent of sows spend a portion of gestation in open pens. Plain surveyed pork operations with 1,000 or more sows. He received responses from 70 operations, which combined own about 3.6 million of the nation’s 5.7 million sows.

Source: Survey Shows Few Sows In Open Housing - National Hog Farmer - 2012

This means that the other 82.7% of sows from these operations spend almost their entire pregnancies (114 days) in small gestation crates.

77% of pigs are castrated without pain relief in 26 European countries:

approximately 20% are left entire, less than 3% are castrated with anaesthesia and the rest are castrated without anaesthesia

Source: Practice on castration of piglets in Europe - 2009

In the USA virtually all males are physically castrated at a young age (predominantly) with no anesthesia or analgesia (pain relief).

Source: Pig Castration - Texas Tech University

Pigs in barren, crowded environments cannot perform natural behaviours and get frustrated, which commonly leads to biting tails on other pigs. Farmers often deal with this by docking (cutting) piglets' tails. EU law requires that pigs are given environment enrichment such as straw for stimulation and are housed well (e.g. not too densely) to avoid tail biting. Tail docking must be a last resort. An investigation found that 44 out of 45 pig farms in 6 countries in the EU failed to meet these legal requirements, by not providing effective environment enrichment and routinely tail docking piglets.

Source: Widespread Breaches of Pig Welfare Laws in the EU Summary Report - 2013

For the 2014 production year, 93 percent of the annual pig crop was produced on operations with at least 5,000 head

Source: 2015 Overview of the United States Hog Industry - USDA