John -
I use epoxy and softex fairly often, silicone on rare occasions. For epoxy, I use a two-part Devcon primarily because it comes in large ketchup squeezer containers.
I use a square of tin foil 4-6" square after being folded over for strength, curl up the edges if you like. Then I use a Starbucks wooden stir stick to blend the two parts together. A scientist at 3M informed me that the two factors that yellow the glue are mixture and UV. You want to get the right mix, then keep them out of direct sun. The wood affecting the color is a myth, 3M provides a wooden stick with their package.
If using 5min, use small batches due to fast dry times. Roll up the tin foil and stick and throw it out - EZ cleanup.
Softex - I only use this to dab, and I close the jar partially after every dip of the starbucks stir stick. Don't leave it unattended, if you do even if it threads ok that day you'll never get it open another day later. Try not to get the stuff on the outside threads of the jar mouth. I dip the stick and remove excess so that it stays on the inside of the jar mouth. I currently have three jars: 1) the one I was careless with, still half full but can't open... 2) the one I was careful with, almost empty and can still open the jar... 3) the one a friend gave me after he read what Tolulene can do to your prospects for having children.
Suffice it to say, the solvent in Softex (also for neoprene repair glues like aquaseal) is highly toxic.
I haven't been using silicone as much as I used to but I suppose it's the safest of the lot. It is not as durable as others but it ls light as a feather and lets you build some really large profile flies with great action - kind of like a plug you can cast with a fly rod.
You need to know about another glue called Zap-a-Gap. When tying coastal SWFF flies, I use it instead of head cement in many cases, including the deep eel. It is tough enough to secure the threads around the weighted eye. Much different than the lacquers I use for steelhead and salmon flies, but in an instant the threads are hard as stone. Don't get any on the fingers, or you'll feel like the kid who put his tongue on the swingset on a cold winter morning.
Tie on!
Juro