My father owned my SE Sport for ten years and I've had it for 2 years now, so I will try and give as much info as I can.
Door seals, mainly the fronts - Lift them up and look for rust, specifically around the front edge near the mirror. Common issue.
Water leak into the boot - Will be worth getting the spare out and checking the wheel well for moisture. Can be anything from a light seal upto a panel seam seal failure. Worth checking.
Boot struts - These fail often on the hatchbacks. Honda have since upgraded them but they are expensive from a dealer. Struts from a Mk3 Mondeo fit straight in, and are a much better alternative.
Rear brake pipes - Most will start to corrode by now, mine included. Will be worth covering these with something when/if you replace them.
02 sensor - Not uncommon. Usually the downpipe one which fails. Easy to change, but will give your wallet a raping.
Sticky rear caliper - Mine was also guilty of this. They are self adjusting calipers that use a spindle setup which pushes the inner pads on to engage the brake. This spindle can seize up. Sometimes you can get lucky and rectify it by freeing up the spindle, but most the time it requires a new caliper.
Windscreen seal -I've had about 10 people come to me in the last month asking me about this, so it seems to be becoming an issue as the car gets older. The windscreen seal fails and lets water get in through the top. Can be solved by either removing and re-sealing the screen, or pulling back the headliner slightly and sealing from the inside.
Knocking from the rear - I thought this was something like drop links or arb bushes. Turns out that on mine (and most others) it was the strut top bushes. Despite having a complex suspension setup, Accords are quite easy on bushes and droplinks.
A/C pump failure - Again, I've had a lot of people come to me with this issue lately, probably due to the car getting older. I've not been able to investigate this fully as I dont dabble with AC systems, but apparently its just a bearing failure.
Engines and gearboxes on these are pretty bullet proof and don't give much hassle. My Accord is a slightly different variant of yours, but alas it has done 165k miles now and hasn't given any major issues. However, there is one more common problem I want to show you which affects all models (CH, CG, CL etc.) and can cause issues, so please read carefully and if need be, check yours.
Water entering cabin - This problem is becoming more and more common. I have pre-checked over 30 Accords that have came to me, and all of them had this issue in varying states of decay, mine included! You will hear lots of people on THAOC or TypeAccord saying there car struggles to start after rain, or that it may start but will cough and splutter until warmed up. Unfortunately, THAOC/TypeAccord is full of nothing but wannabe mechanics, and they will suggest everything from spark plugs to bloody air filters.
Unfortunately 9 times out of 10 the problem is more serious. Honda in there infinite wisdom, decided that when water runs behind the strut tops in the engine bay, it will have nowhere to drain (thus pooling up) and eat through the firewall, getting into the cabin. Water would then saturate the soundproofing, cause condensation to get onto the ECU's. The condensation causes the ECU's to act up (which cause the rough running/non starting) and they will continue to do this until they dry out. If you want to check yours, you will have to remove part of the front arch liner it's quite simple.
You will need a standard phillips screwdriver and a small flathead.
1. Remove the 3 screws that go into the sideskirt, and the rear half of the clips from the liner.
2. Peel back the liner and look for any rust where the inner arch panel joins the firewall. Give it a good poke if need be.....Giggedy.
Have a look at the build thread of my own Accord. You will see me mention the rust issue as I had to get it sorted. The pictures should give you an idea where the rust could be.
I hope that helps. If you have any questions, feel free to e-mail me!