Thru-hiking southbound on the Pacific Crest Trail is generally accepted to be more difficult than doing the same northbound. There are many reasons for this outlined below. People who choose to hike southbound generally do so because of some time constraint. Some college students, for example, may not get out of their Spring semester until mid June. That means they cannot start out at Campo with the rest of the northbounders in April/May, so getting to Canada before the first Fall snow is chancy at best.
Whatever your reason for choosing to hike southbound, there are some things you should keep in mind while planning your hike.
Start dates: Southbound hikers tend to begin their hike June 15 or later. This is based on the average time it takes for the snow to start melting in the Cascades and for the PCT to become (somewhat) navigable by hikers. Southbounders don't want to start too late either. Far off in the distance are the High Sierras. Southbounders need to be sure they can get through the High Sierras before the first Fall snow. A good rule of thumb: aim to arrive at Kennedy Meadows by October 1st. The severity of the prior winter and the temperatures of the spring season can play a big role in when you start your southbound hike. Setting a general date - but being flexible about it right up to the last minute - is a good strategy.
Border crossing issues: Southbounders face a different situation than northbounders with regards to border laws. Though it is possible to obtain a permit to enter Canada along the PCT, it is not possible to obtain a permit for entering the U.S. along the PCT, even if you are a U.S. citizen. Entering the U.S. along the PCT is considering 'entering the U.S. without passing inspection' - a federal crime. There is no legal way to do it. Some do it anyway - as enforcing this law out in the backcountry is very difficult. They do so at their own risk. Other's start at Hart's Pass, head north to the border, touch Monument 78, then turn around and hike south to Mexico. Still others just start at Hart's Pass and start hiking south. The decision is yours, of course.
Navigational issues: Navigating the PCT southbound is much more difficult for southbounders than for northbounders - especially for the first 500 miles. The trail is routinely covered with snow, sometimes for more than a mile. This makes navigating the PCT with just a map and compass very difficult and time-consuming. PlanYourHike.com strongly recommends southbounders take a GPS - at least for the first 500 miles. Southbounders don't have any footprints to follow through the snow, and it is very easy to end up lost. You may also notice that some areas seem to have more PCT emblems nailed in places that are easy to see when heading northbound, but difficult or impossible to see heading southbound. Far more so than northbounders, southbounders have much to gain by packing a GPS device.
Hiking hours: Soutbounders start their journeys around summer solstice, so they have fewer and fewer daylight hours for hiking each day. This may mean you end up starting earlier in the morning or hiking in the dark in the evening. Night hiking with a good headlamp can be very enjoyable.
The dry desert: The desert is sometimes cooler in the fall than in the spring. But (unless it rains), it is almost always drier. Checking the water reports, and knowing where the water is in the desert can be crucial to a safe and successful hike. The popular water caches (maintained by trail angels) may be dry when you get there. You may want to call ahead and ask if any of the trail angels would be kind enough to fill them up for you. You may also consider using GPS to load all the waypoints for known water sources in the desert along the PCT. Also, the Forest Service shuts down many water faucets beginning November 1st of each year (so the pipes don't break when they freeze). But hiking 700 miles through the desert in 30 days is pretty easy at that point.
Thru-hiking window: Northbounders typically have a window of about 6.5 months to hike the entire PCT. Southbounders have closer to 4.5 months (roughly June 15th through November 1st). This means fewer zero days and/or longer hiking days. Since you'll have to 'hit the ground running', you'll want to make sure you're in decent physical shape before you hit the trail, since you won't have the luxury of getting into shape along the trail.
Other Notes for Southbounders
Solitude: At the start of their trip, southbounders have the trail all to themselves. It is common to hike for days between two resupply points without seeing a single other hiker. Yours may be the only footprints in the snow, and it may seem like you have all the Cascades to yourself.
The northbound pack: Somewhere around the Oregon border southbounders start to cross paths with the northbounders. After several hundred miles of solitude, it can be quite a joy - and a shock - to meet the northbounders. By that time, the northbounders will be almost finished with their hike. They'll have been on the trail for four or five months. They'll be thin, strong, dirty, smelly, and have smiles from ear to ear. And you'll meet every single one of them.
Travel though Oregon can be slow for southbounders. Almost every single northbounder will want to stop and talk to you. They'll want to know what other northbounders you've met, and how far ahead they are (which, so you know, is roughly twice the distance you've hiked since you've seen them). They'll ask about distances, trail conditions, trail magic, and why you're hiking southbound. Some will ask you to pass along a message to another northbound hiker further behind them. Meeting all the northbounders is a ton of fun, but it's also very time consuming. You may want to keep this in mind when estimating your hiking speed through Oregon. If you keep the conversations brief, you can easily pull off many back-to-back 30 mile days in Oregon.
Fewer bugs: Southbounders tend to experience far fewer bugs than northbounders. That doesn't mean you should leave your mosquito netting and DEET at home, but it is a good reason to rejoice.
Less rain: Southbounders tend to experience less rain than northbounders. You may keep this in mind when considering what kind of shelter and rain gear you plan to pack.
Hiker Boxes: After you pass the northbound pack you'll see all the hiker boxes loaded to the brim. Muir Ranch will have enough hiker box food to feed an army - certainly enough for you to resupply there without having to send a mail drop there (which costs about $50). It may not be the best food in the world, but it can save you a ton of weight and a good deal of money. Naturally you should look before you leap. Give Muir Ranch a call before you head out of Tuolumne Meadows and ask how full their hiker boxes are.
About 10% of PCT thru-hikers hike southbound. If you like being in the backcountry alone, you tend to hike more miles than others (25 or more per day), and you feel comfortable navigating in snow, then southbounding should be a fun experience for you. Keep the above tips in mind, and enjoy your hike!