The way in which equipment and resources in general are handled by Spycraft has always been a little odd. In real-world espionage, an agent going on an operation is treated in one of two ways, he either is rather grudgingly handed minimal kit and is expected to get on with it or (if his agency is desperate to get the job done) he will have equipment and resources galore offered to him and anything else he needs he'll merely have to ask for... Yet the core rules offer systems of 'gear picks' that require a fair bit of resource-juggling when preparing for a mission. The one bit the rules got 'right' (in real-world terms) is that agents are expected to return everything they've been issued, or account for its loss.
Here is an assortment of ideas designed to enable agents to build up, over time, their own personal (and personalised) equipment - something real-world spies like to do - and even to profit from their adventures materially. After all, not every agent is playing the Great Game out of pure patriotism or even a love of excitement. Here three mini-systems are presented which can be used in conjunction, or you can pick which ones suit your game style and discard the rest. The three systems are the Stockpile system, the Cash'n'Carry system and the Loot system. Depending on which you use, campaign characterists may change as well as the way in which equipment and other parts of the rules function.
The Stockpile system lets characters keep any item with which they are issued on a permanent basis, rather than having to hand it in every time they return from an operation. If you use the formal Intel Phase, that remains (but can be dropped if you prefer), and characters are still limited as to what they possess. Anything designated as a Restricted item cannot normally become a personal possession and will still be loaned out, if you're lucky, when the nature of the operation indicates that it might be of use. The agent's regular equipment is determined at character creation, by rolling Possessions and Gear Picks together and converting the Gear Picks to actual items. Any option taken that provides an item or an extra Gear Pick is included in the total at this point. At the end of a mission, the stockpile refreshes, i.e. anything lost is replaced. It's still a very mechanical system but it does allow for some continuity.
The Cash'n'Carry system caters to those who prefer cold hard cash to abstract gear systems. Gear picks are translated into monetary terms, and characters then have to purchase what they want with that money. Again, this system can be used to allow characters to keep a core or regular equipment (hence you use either Stockpile or Cash'n'Carry, not both). Characters now have to pay for their Lifestyle choice on a regular basis (rent, grocery bills and the like) but they receive a regular income as well as 'starting cash' with which to do so. They can even save - or splash out - as they please. Again, Restricted items may not be acquired during initial purchases, characters will need to get hold of any they want during the course of play - and if not stealing them will have to pay for them. When it comes to a mission, characters receive a sum of money (wages, expenses, term them what you will) that can be used to purchase items required for that mission and to pay regular bills. Characters may also be required to pay for training. It is still a mechanical system, but some players may prefer the added realism of thinking in terms of money. It also makes it easier to add in new items of equipment provided you can find a real-world price for them. Even if, like me, you live somewhere you cannot go out and purchase firearms legally, there's always the Internet to research overseas gun stores for tasty new 'toys' and their prices!
Finally, the Loot system accounts for all those Restricted items that a character may want to acquire and hang on to but which both the core rules and the rest of the material presented here do not permit. Again, however, it is a rather mechanical system with artificial restrictions, whither you are using Stockpile or Cash'n'Carry to determine what characters normally have.
It all depends on how you want to run your game. If you like cinematic spies, consider how James Bond always stops in to see Q before a mission (and sometimes has a mid-mission 'care package' delivered if the need arises)... and cash never seems to be a problem, except possibly at the gaming tables. If your style is more realistic, how much cash and gear people have needs to be monitored more closely although incomes may be generous. Using a mechanical system is one way to keep checks and balances on what characters may have, but can detract from enjoyment as well. There are interesting ideas here, consider them carefully and use what works for your group.