Romans definitely had metal, and in some archaeological sites the nails are all that remain of wooden structures. Here's a paper analyzing the nails found at a dig at Inchtuthill in Scotland, where the Romans had a fort during the time of Agricola. It's pretty dry reading, but it does give some good information about the manufacture of such nails, as well as placing the nails within the larger archaeological context, giving a good overview of the amount of iron used to make nails, that kind of thing.

Roman woodworking relied heavily on mortise and tenon joinery. Shipwrights in particular used some fairly complex scarf joints. We don't know whether such scarfing was used to make composite beams for timber roof spans, although it is not out of the question.

Various types of adhesive were also used for woodwork, veneer and marquetry; animal glues in particular. Pitch was also used, as was plaster, depending on the application.

Wooden pegs and dowels were used in some joinery. Copper alloy T- and L- nail-plates were also used to reinforce joins, particularly in furniture and fixed furnishings. Roman nails are most often associated with metal hardware like this. So in other words, they saw limited use outside of certain architectural applications.

Iron staples and brackets were used to affix finish carpentry elements and marble veneer to walls. Bronze, iron, and lead ties were used for ashlar masony joins.

I think that about covers the basics. If you've got any more specific questions, feel free to ask.