When I do toner transfer home-etched boards, I just don't remove the toner after I have etched it! The black sits over the copper just like a soldermask.
It burns/boils away from the pads when you touch the soldering iron to it. It seems to have no effect on the electrical or mechanical properties of the joint.
Are you just trying to make it look prettier? After it's all done you can probably use any sort of spray clear-coat on the solder side, but I wouldn't do that before soldering on components. There are some spray-on coatings that serve as flux (http://www.lpkfusa.com/Store/ProductDetail.asp?ProductID=107) plus LOTS of special-purpose "conformal coatings" designed to protect PCBs from all sorts of highly specified environmental "issues", but they tend to be very expensive.
There are also assorted products for tin-plating your PCB.
Frankly, if you're going to solder your board relatively soon after making it, I don't think any of these are worth the trouble. While the copper traces will oxidize on the surface, the oxide is a bit like Aluminum oxide - it's protective of the remaining copper, and the PCB will stay in working condition for decades (while at least one of the tin plating products I was looking up contains exactly the sort of fluxes that you are NOT supposed to used on electronics...) It'll just look not so pretty...
I don't think I've ever seen a home fabrication friendly soldermask material that actually works as a soldermask (ie holds up to soldering heat on nearby parts of the trace.) THAT I'd like to find (I think "real" soldermasks tend to be 'cured' epoxy-like things, nasty and difficult to deal with in home environments...)
I've considered using high-temperature spray paint and then etching off the solder pads with the laser cutter at Techshop. Haven't tried it yet, and it's not exactly a technique that could be used in any home PCB fab, but interesting anyway.