noob qestion

As a guild wars noob I now have several characters in various starter areas. If I miss some of the quests in the starter area (difficult to find a group in prophecies) will this affect anthing later on in the game?

No. Many of the side quests are just that. They are tangentially related to the story line but they are entirely optional. The 25 Prophecies missions are the core of its story arc. Everything else just adds depth. If you want to pay attention to all the lore, do them. If you want to progress through the story quicker, skip 'em.

In Factions and Nightfall, you can't move on to the next areas until you complete the current primary quest. If you can move on, you've done what you had to. If you can't, check your quest logs under "Primary Quests" to see what you need to do to move forward.

Other than quests that take you to the next mission, you can skip about everything. In prophecies I would do most of the quests you get early on because they give you skills. Having them unlocked on the account can be of great use once you get heroes.

Unless you mean in pre-searing (the green and pretty place), you can always go back and do the Prophecies side quests later. In fact, when you are able to change secondary professions, there are always a few that become available that you couldn't get before. Here is a link to the wiki page for Prophecies missions and primary quests http://wiki.guildwars.com/wiki/Prophecies_Missions

The only ones you MUST do are all related directly to the storyline and will be listed under Primary Quests in your quest log. You cant advance without doing those.

Secondary quests are optional.. they are available, but they are not required to advanced. Those are mainly just filler quests for helping you level up. leaving pre-searing in prophecies will cause you to lose any quests you had there, but if you were strong enough to get out of there then you dont really need them anyways and can continue on from there.