All,
This pertains mostly to the 5th gen, since so many people have them, but I suspect the 4th gen is susceptible to this problem, though I haven't heard of many complaints.
The absolute most common problem with the 5-speed has got to be the 5th gear grind. It would also seem that as this problem gets worse, reverse eventually becomes difficult to engage (especially when hot) and eventually goes out completely. I know several people this has happened to, me being one of them.
I know now why this occurs; after lengthy analysis while repairing a '98SH 5 speed tranny, the problem is obvious.
Here are the parts:
http://www.ntpog.org/articles/5g_tranny/Img_4866.jpg
And here's reverse:
http://www.ntpog.org/articles/5g_tranny/Img_4867.jpg
Here's a closeup of the 5th/reverse fork interaction (in neutral):
http://www.ntpog.org/articles/5g_tranny/Img_4871.jpg
Here's how it works. Note that the 5th gear shift fork moves down to go into 5th, but has to move up in order to actuate the reverse shift fork (though it doesn't do anything with 5th gear):
http://www.ntpog.org/articles/5g_tranny/Img_4872.jpg
Here it is in 5th:
http://www.ntpog.org/articles/5g_tranny/Img_4873.jpg
http://www.ntpog.org/articles/5g_tranny/Img_4874.jpg
And finally, in reverse:
http://www.ntpog.org/articles/5g_tranny/Img_4875.jpg
http://www.ntpog.org/articles/5g_tranny/Img_4876.jpg
Now, what does this mean? Well, as you munch 5th gear, the synchro sleeve takes a beating. As you may notice it slides over the hub to engage with the 5th gear mating teeth and lock it on the mainshaft. OK, but the sleeve doesn't mate to anything in reverse. Well, it has to move up off of the hub in reverse, though- which can't happen if the teeth have mushroomed out such that the sleeve binds on the hub:
http://www.ntpog.org/articles/5g_tranny/Img_4878.jpg
http://www.ntpog.org/articles/5g_tranny/Img_4879.jpg
This is what happens. It's all that happens. If you happen to get reverse engaged halfway and you grind, QUIT! Grinding reverse will damage the reverse gear on the countershaft and damage the mainshaft itself (reverse is machined directly into it). What happens is that the idler gear doesn't drop down all the way, and all the reverse gears just grind. You can also widen the "pinch" of the reverse shift fork on the idler gear, which will mandate replacement of the shift fork.
What's the fix? If reverse quits and everything else is OK but grinding in 5th (or you *just* have grinding in 5th), you can just replace the reverse synchro pack. This is pretty easy as it doesn't require mainshaft/countershaft removal, just removal of the reverse fork and you can "work" it off (moving the 5th gear shift fork out of the way).
I thought this would be handy for some of you, if not for repair, then for peace of mind. I know I'm glad to finally know WTF was going on inside of the gearbox. @#$%! Honda and their brittle transmissions.