This is a no brainer, really.
You take the combi-weapon. Always.
If you are a Librarian, you are charging into close combat, or you are a waste of your points. So why pay for a storm bolter, if you are going to be in rapid fire range anyways?
Also, combi-weapons are not intended to be weapons that serve two functions, so stop saying "oh buy I only get one shot per game so it isn't worth the points!".
Combi-weapons are for shots of opportunity. You are paying 10 points for a shot that can potentially change the course of the whole game!
As far as the best combi-weapon goes, I would give it hands down to the combi-melta, followed by the combi-flamer, and lastly, the combi-plasma.
The melta gives you a damn good chance at pasting that Land Raider full of scary things, and then charging its contents in the same turn and MOST LIKELY wiping them out.
The flamer is great for the fact that since you only get the one shot with your gun, you KNOW it will not miss. Its a guaranteed hit. Who wouldn't pay 5 points for a guaranteed hit template weapon? Really comes in handy when theres a big scary mob of genestealers in front of you, who are ready to rend through your 2+ armor save at initiative 6.
The plasma? 2 shots? Well I guess thats cool. But they can hurt you back...
Still not as good as the others, even when double tapped.
Also, did you say something about equipping one with a plasma pistol? If i recall correctly, models in termie armour have a VERY small selection in the armoury, and I don't think any type of pistol is included amongst those.
How can some one who plays Space Marines not know that termies can charge no matter what weapons they fired?
And as far as the argument of not taking them because they distract you from what the librarian is supposed to be doing (killing multi wound, high toughness models ). NEWS FLASH, things don't always go according to plan.
And anyone who gets distracted from the librarians primary role by a single combi-weapon in-game, is probably going to lose anyways, and probably deserves to lose.
Unless you are really trying to save points, the combi-weapons shine compared to the storm bolter.