Here is my favorite tripper all set up with the cockpit pump, thigh straps, inflatable lumbar support, surf leash, stronger rudder and all the other outfitting I've done to make it work just a little bit better.
Seat height and width
The basics of comfort for me start with my bottom being about two inches higher than my heels for all day comfort. I can get away with less for short surf sessions or quick trips of an hour or two but one really long multi-day trips I want to be at least two inches higher than my heels and more is better. To accomplish this I usually add an inflatable camping seat to the kayak or a foam hot seat with extra foam glued underneath. I usually have most of my seats Velcro attached to the boat so I can take them out or move them around. If it gets really rough I may remove the seat for increased stability for a couple hours. The high position is more comfortable and it increases my sprint speed by up to 0.5 mph, so I think the body mechanics are much better.
Sometimes I've noticed that a seat that seems too narrow is much improved by adding a hot seat pad which raises the height and flattens the bottom of the seat making it better fitting for wider bottoms.
For back support I like an inflatable lumbar support. Sometimes I use a foam lumbar support, especially in a sit in side boat. Most boats have built in support or a bulkhead to attach foam, but some boats like surf specific sit on tops have nothing. In that case I like the low back bands sold here at Topkayaker.net:
I usually wear shoes while paddling because I have to get out in a lot of rough places so I no longer glue pads to the bottom of the boat where my heals rest. However I still have replaced the footpegs with a foam bulkhead in one boat and added padding to the foot bar in another boat. I really push hard with my feet when paddling and the padding really helps.
I don't know whether it should be called knee supports instead but I use straps in a sit on top and sometime add a quick release seat belt is I know I'll be in really rough stuff and want to be certain I stay connected to the boat. Wave skis usually only come with seat belt straps because they work best in the surf. Don't add a seat belt strap to your boat without expert help. If you do it wrong it might not hold you down when you want and if you do it really wrong you might get trapped upside down!
Thigh or knee support in a sit inside is easy. I like a high deck because I keep my knees bent, but I want it padded to where I can still lock my self in and attempt to roll back up or get an Eskimo rescue. If you do not want to fiddle with cutting gluing in foam there are seal adhesive pads available in kayak shops.
I know a lot of people want a boat with a wide seat, but I like it pretty snug. I find a seat that fits right against my hips is comfortable even if it has no padding. A snug fit does a lot to help you edge the boat just the way you want.
In boats that get occasional drips in them I like a simple foot operated pump that is a simple bulb on each foot peg. On boats that can really flood I prefer an electric pump. I still have boats I use with a hand pump.
Unless it is a surf or white water specific boat you should outfit it with a sail for fun and increasing your daily mileage. Most of the time I mount my sails by using a Scotty fishing rod holder. Under most boats not designed for fishing you will need to add 1/2 wood or plastic under the deck and through bolt your mount though the deck and the backing block. A sail mount pulls on the deck just like a big saltwater fish so do not underestimate what it could do to your deck. Think tarpon rod not bass rod mounts.
If you paddle a sit on top in the surf you need a leash so you can slow the boat by holding onto the paddle. Sit in sides fill with water and slow down a lot as they wash in. Sit on tops come into the beach like an out of control jet when the pilot is ejected. You owe it to the swimmers and other surfers to control your boat. Get the kind that coils or the kind with bungee inside webbing so you avoid tangles and strangles and get some lessons from other good sit on top surfers before you use it. I paddle leash is often not recommended for sit in side surfers or paddlers but sit on top paddlers should use a leash.