I am normally in the same boat as you. Stay on site so we have express but a lot of the bigger rides I ride solo.
Normally (about 90% of the time) the express line is always the best option. The reason for this is some rides (like the mummy, MIB, Spiderman, Transformers, etc) during busy parts of the day have an entire loading station set aside for loading Express guests. The only time the normal line goes into that loading station is when there are NO express guests in line.
Now, the single rider line can use both sections of the loading area. However, you are at the mercy of other guests. You have to hope there are a lot of groups of 3 (or in the case of MIB 4 or 5). On top of this, you have NO choice in where you sit if you pick the single rider option. Finally, your line might move one or two people per dispatch (or not at all) while the express line might move 12 people or more each time.
We have tested Spiderman before during peak times. Normal line had a posted 120 minute wait. The express line was backed up to the first room you enter when you go into the building, and single rider was fairly short. I was able to ride the ride twice in the express line before my friend was able to get on the ride once while she waited in single rider. When express guests are in the same room as single riders, that line never moved from the time I entered the room until the time I was out of the room and loading at the station.
Your paying for the perk (in a sense) so you mine as well use it! It is extremely rare to have a shorter single rider line than an express line. Even if the single rider line looks short, you might be standing around a while if no single spots are needed.
