I've covered the process for cleaning your fly rod before & you can read all about it on the "Tackle Tips" page of this website. However, I'd like to add a little more explanation for those really dirty rods.
What you want to do is remove all the dirt. That's vital. A lot of folks give the rod a quick wipe down & figure that's good enough. Well, that's what you should do after every day fishing, when putting the rod back in the tube at the end of the day. I'm talking about giving it a good, thorough cleaning. With a soft cloth & a gentle liquid glass cleaner (the blue stuff), give your fly rod a good cleaning. You're also going to want to use some cotton swabs to clean the line guides & the corners of the guides & wraps. Take your time & be very thorough. You don't want any dirt left at all.
Now that you've got all the dirt off the rod, let it dry. This next piece of advice is for really used rods - those that have seen better days. Take a good paste wax - the kind made for use on cars & autos & gentle apply it to the rod. Let it haze over & then gently remove it with a clean rag. Again, use cotton swabs to get the wax out of the line guides & their corners. Make sure you remove all the wax. Now what you'll find is that, for a little while, the more you gently buff the rod shafts, the cleaner & shinier the rod will become. So be sure to polish the rod a lot after you've removed the wax.
In choosing a wax you want to make sure that you don't use a wax that has cleaners or other chemicals added. Some are made with these additives for alder cars. You don't want that here. What you're after is something called carnauba wax, which can be found at any auto parts store. Make sure that you spot test the wax on the rod before you coat the whole thing. The butt area just above the grip is a good spot to do this test.
This method works very good on graphite, fiberglass, & bamboo fly rods that do NOT have a matte finish. You can apply wax to a matte rod, but you will loose some of the matte effect. The best part of doing this is that in the future you're going to find that water & dirt just slide off the rod & that your fly rod is going to look & stay cleaner than before. Taking care of an older rod will give you extra years of service from it & help you get even more out of your investment.