OK - so, continuing on my background a little - I'm run the IT dept. for a multinational company with branch offices throughout the US and Latin America - so I set the standards, and over the years I've done a lot of the wiring myself and hired lots of vendors to do the offices too...
About 7 years ago I started the less-common but incredibly versatile trend of running Cat5e only to every office... A cube gets 3, an office gets 3 each on two opposing walls. I was just tired of having to grab tools to move phone lines, extensions, etc - and I was lucky enough that all of our offices have expanded over the last 5 years so I've gotten to re-wire every one in this fashion. Generally I fly to the site to manage the install and hook up the basics, then head home (I should send one of my guys, but I don't have anyone with the networking and telecom knowledge I have). The great thing is, because things are labeled and I keep pictures, even if I leave and they decide to reconfigure where their digital phones are, fax lines, and PC's, I can generally walk an unschooled admin through any change. And, I've never had to add wires to a single office again. Using the Cat5, I can pump video, powered ethernet, analog lines, digital lines, powered polycom phones, and anything else you can imagine through the Cat5. When sending a phone through, just use an RJ11 and it'll do just fine. You can also use RJ45 patch cables for phones if you're patching around a wiring closet - it doesn't make a difference - they're just more expensive.
In the past before I had laid the wires, or in extreme circumstances, I've done some trickery where a digital desk phone, an analog phone line, and a 100BT ethernet connection have all run through a RJ45 jack using splitters at the patch panel and jack. They also sell some standard splitters that'll let you run two 100BT connections over a single Cat5. Even today I showed someone how to send 4 phone lines over a single Cat5 through a single jack, then made a patch cable that was an RJ45 on one and and 4 RJ11's on the other end (dense modem-boards where I don't want 8 phone lines into a 1U server) just to make things cleaner.
Amazingly, your background is what causes the confusion - most people don't know the difference between RJ45, RJ11, USOC, or anything else - it's a modular-looking plug, and they'll try to plug anything that looks like it'll fit in it... I've learned that from years of working with not-so-bright users. Honestly, stick with the RJ11 or RJ45 using T568A or T568B (I'll only use the latter, but it doesn't matter as long as you're consistent on both ends) - and you'll never have an issue. For phone lines, they even sell some cool splitters which break out the lines and give you different combinations of Line1 & Line2 in different places, and Lines 3 & 4 on the primary pairs, etc. (RJ11 is meant for 2 lines - line one on the inner pair, line 2 on the outer pair - 2-line phones expect that).
One thing that does make things easy is keeping standards - we only use Siemon jacks (not the common Leviton) because they have a slot on top that lets you slide different indicators in (and you can order all types and colors) - that combined with standard cabling colors to differentiate between each type and you should be fine.
Also, I've been lucky - never once in any office has plugging a phone into a switch or weird things like that caused a problem... just in the old days when analog modems into digital phone lines did I see issues where the modem got cooked.
I could probably go on and add more, but I'm being handed the baby... so let me know if anything needs more details or clarification.
. I.e., you could use something like "LR-01-02-01" which could mean "Living room, wall 01, outlet 02, jack 01".
