Well, first off I have a 1.6 SE, 54plate so can help you out a wee bit.
The bearbox issues with the EP's are mostly either bearing or syncro, one of my gearbox bearings is worn some-what but it hasn't failed yet, still going strong after years of it being noisy. That may help with the gearbox thing but do bear in mind, other major faults can develop with them but it's not very common compared to the above issues. Other common ones include:
Driver's window issues - they eventually go wrong for alot of owners and when, especially in wet weather, you put the window up, it will go up around 3/4 of the way, then stop and go back down to about half way. The window shifts forwards and backwards so I can assume it comes out of it's runners and some owners have said the runner ball joint pops out or something along those lines. It does it on mine but some H5 silicone spray down the channels and it's fine.
Clutch squeak - VERY common issue, it's not going to make the clutch fail or anything, it's just annoying. Mine does it and all I did was spray H5 into some openings as directed by owners and it goes away for a long time, eventually comes back. My mechanic said he has to disassemble the box to grease the bushing at the clutch slave cylinder but it will cost and it's not worth doing (his words).
Squeaky throttle pedal - Again, just very annoying. Only does it at the flack end of the pedal (the loose, free-moving bit before the throttle is pushed/engages 'bite').
Noisy brakes - Mine squealed and all sorts, annoying noises that you usually hear when your pad wears down to the squeal bar. Paid £90 to have all my brakes stripped down, cleaned and put back together. Stopped the noise but my brakes not wanting to be defeated, decided to develop a different noisy characteristic so I gave up.
Noisy seat - Usually passenger for most people and the same for me. If somebody is sitting in my passenger seat (rare) while im driving, the seat squeaks when you hit uneven ground or potholes.
3-button functions - above the gear stick are 3 buttons, rear demister - A/C - air circulation. they light up when you switch your side/head light on (logically
) and they can sometimes not light up, seems to be a small issue in terms of how long that lasts, mine used to do it often but now hasn't done it for years. If they don't light up just give hard taps around the bottons and they'll light up, bit odd and a few have had issues with this.
Crap paint - same with most edition Civic's, Honda used thin, crap paint so they are very easily marked or chipped, something you have to live with unfortunately. I paid £300 to have chips and scuffed resprayed, then a week later, more chips in the bonnet
, Give up!!!
Milano Red - VERY common problem from old to new Civic's. Milano is an oil-based paint and it seems to vary hugely whether people get the 'Milano Pink' problem. All the metal panels on the car fade, leaving red skirts, bumpers and spoilers but pink bodywork. Common problem since they started doing Milano red in the 80's (I believe) and they still haven't bothered to sort it in newer paint technologies or releases. Under synthetic light or sunlight it looks awful but in the dark or when it's raining, you won't be able to see the problem. Some say a MOP can bring it back, others say it's a top-coated paint and the paint UNDER the lacquer has faded so can't be mopped unless you remove the lacquer cost to get the to the paint underneath, but then it would need to be re-lacquered. Alot of mixed opinions on this and still no concrete proof a MOP works.
I think that's basically it my friend, there may well be other issues but if there are, I don't think they fall in the 'Common' problems list.
I'm signed up to EPCIVIC.COM and they're fantastic, real nice bunch and a fantastic forum dedicated to EP owners (EP1,2,3,4). Any issues or anything you need to know, it will be on that forum as they're owners and know everything about their cars.
*Not trying to get people over to another forum, just informing of a forum dedicated to EP owners. please don't ban me*