SIGCOMM (the major networking conference) will be taking place shortly. Although I won't be attending, I thought I'd mention some of the papers that involve theory in a non-trivial way. This list is not meant to be exhaustive, so I apologize for (and welcome comments on) anything I might have missed.
The networking community, I've found, is very amenable to theory. I think there's a real understanding in the community that obtaining systematic improvements in something as wild and large as modern networks requires a solid, fundamental grasp of what's going on. This means good models, and good algorithms and data structures. This doesn't mean that SIGCOMM is full of theory papers; they generally want to see some sort of implementation to see that whatever idea is presented actually works. But many papers have a non-trivial theoretical component, and the SIGCOMM conference is certainly a good place to look for important problems where theoretical insight would be welcome. (The same is true for the larger networking conference, INFOCOM, but that conference is so large it's harder to get a handle on. Also, SIGCOMM aims to be a bit more visionary, or "out there", which I think means there's more opportunity for theory to get involved.)
DTN Routing as a Resource Allocation Problem: DTN's are Disruption Tolerant Networks -- in this paper, focusing on mobile nodes that are only connected intermittently. In one section, the paper sets up an appropriate graph model for the problem, and proves lower bounds for various situations. For example, any algorithm that doesn't know the schedule of node meetings is Omega(n)-competitive compared to an offline adversary when n packets are to be delivered. The paper then moves on to heuristic approaches and an experimental evaluation.
Orbis: Rescaling Degree Correlations to Generate Annotated Internet Topologies: The paper considers the problem of how to generate realistic Internet graphs, where here the relevant graph is a router graph with nodes labeled to give the corresponding AS (Autonomous System) network.
An Axiomatic Basis for Communication: Pretty much like it sounds. Trying to set up a basic logic for network protocols, covering issues like naming, binding, forwarding, etc.
Embracing Wireless Interference: Analog Network Coding: Normally, we think of networking coding as XORing packets, or taking random combinations of packet data over some finite field. In wireless, you may be sending signals, not bits. What do you do then? This paper looks at the problem of effective algorithms for this problem.
Again, these examples aren't exhaustive; many other papers have Lemmas and Theorems in there. In fact, I'd wager that having words like "Lemma" and "Theorem" in the paper is positively correlated with acceptance to SIGCOMM. Maybe someone on the PC will confirm or straighten me out. In any case, I'll be giving all the SIGCOMM papers a closer look....